Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xch Working: n-1-38.cluster.ucsf.bkslab.org:/scratch/xiaobo/45881/xch-8058115.60 Result: /scratch/xiaobo/45881/xch-8058115.60 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xch 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/xbc/inputs/xch mkdir: created directory `/scratch/xiaobo/45881' mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60' /scratch/xiaobo/45881/xch-8058115.60 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/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/45881/xch-8058115.60/working' mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/protonate' Storing results in /scratch/xiaobo/45881/xch-8058115.60/finished Working in /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 /scratch/xiaobo/45881/xch-8058115.60/working/protonate /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Using inputs as protomers/tautomers. No processing done 461 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/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Bulk generating 3D conformations all protomers in /scratch/xiaobo/45881/xch-8058115.60/working/3D mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/45881/xch-8058115.60/working/protonate/xch-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 ZINC001735734017 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building' mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001735734017 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/1 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001735734017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734017 none CCOCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 48, 37, 28, 27, 10, 27, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 50, 50, 50, 50, 50, 48, 48, 37, 37, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28, 28, 28, 28, 28] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 235 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734017 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/finished' Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734017 Building ZINC001735734024 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734024 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/2 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O) `ZINC001735734024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734024 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/3 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O) `ZINC001735734024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734024 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734024 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 Building ZINC001735734024 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734024 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 2) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O) `ZINC001735734024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734024 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 3) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O) `ZINC001735734024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734024 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3ccccc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734024 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734024 Building ZINC001735734169 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734169 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/4 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O) `ZINC001735734169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734169 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 22, 22, 44, 44, 44, 44, 44, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 44, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/5 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O) `ZINC001735734169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734169 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 20, 20, 46, 46, 46, 46, 46, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 46, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734169 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 Building ZINC001735734169 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734169 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 4) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O) `ZINC001735734169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734169 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 22, 22, 44, 44, 44, 44, 44, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 44, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 5) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O) `ZINC001735734169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734169 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2scnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 20, 20, 46, 46, 46, 46, 46, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 46, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734169 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734169 Building ZINC001735734175 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734175 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/6 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001735734175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735734175 none CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 32, 50, 50, 50, 50, 50, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/7 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001735734175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735734175 none CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 31, 14, 6, 14, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 31, 50, 50, 50, 50, 50, 31, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734175 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 Building ZINC001735734175 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734175 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 6) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001735734175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735734175 none CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 32, 50, 50, 50, 50, 50, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 7) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001735734175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735734175 none CCc1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 31, 14, 6, 14, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 31, 50, 50, 50, 50, 50, 31, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734175 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734175 Building ZINC001735734176 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734176 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/8 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001735734176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735734176 none COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/9 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001735734176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735734176 none COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 8, 22, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734176 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 Building ZINC001735734176 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734176 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 8) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001735734176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735734176 none COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 9) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001735734176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735734176 none COc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 8, 22, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734176 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734176 Building ZINC001735734203 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734203 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/10 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O) `ZINC001735734203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734203 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 14, 14, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/11 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O) `ZINC001735734203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734203 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734203 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 Building ZINC001735734203 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734203 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 10) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O) `ZINC001735734203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734203 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 14, 14, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 11) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O) `ZINC001735734203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735734203 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3n[nH]cc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734203 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734203 Building ZINC001735734204 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734204 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/12 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001735734204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734204 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/13 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001735734204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734204 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734204 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 Building ZINC001735734204 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734204 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 12) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001735734204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734204 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 13) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001735734204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734204 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734204 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734204 Building ZINC001735734229 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734229 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/14 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1C) `ZINC001735734229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734229 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/15 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1C) `ZINC001735734229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734229 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 11, 28, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734229 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 Building ZINC001735734229 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734229 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 14) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1C) `ZINC001735734229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734229 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 15) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1C) `ZINC001735734229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734229 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 11, 28, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734229 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734229 Building ZINC001735734251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/16 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/17 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 Building ZINC001735734251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 16) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 17) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734251 Building ZINC001735734252 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734252 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/18 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734252 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/19 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734252 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734252 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 Building ZINC001735734252 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734252 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 18) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734252 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 19) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O) `ZINC001735734252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735734252 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccc(F)cc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734252 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734252 Building ZINC001735734259 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734259 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/20 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C) `ZINC001735734259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735734259 none Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/21 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C) `ZINC001735734259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735734259 none Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 20, 9, 20, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734259 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 Building ZINC001735734259 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734259 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 20) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C) `ZINC001735734259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735734259 none Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 21) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C) `ZINC001735734259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735734259 none Cc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 20, 9, 20, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734259 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734259 Building ZINC001735734318 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735734318 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/22 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/23 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/24 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/24' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/25 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/25' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734318 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 Building ZINC001735734318 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735734318 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 22) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 23) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 24) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 25) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734318 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 Building ZINC001735734318 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735734318 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 22) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 23) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 24) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 25) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734318 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 Building ZINC001735734318 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735734318 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 22) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 23) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 24) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 25) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001735734318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735734318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735734318 none C[C@H]1CC[C@@H](OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734318 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734318 Building ZINC001735734441 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734441 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/26 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O) `ZINC001735734441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735734441 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 15, 15, 15, 15, 29, 29, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/27 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O) `ZINC001735734441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735734441 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734441 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 Building ZINC001735734441 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734441 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 26) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O) `ZINC001735734441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735734441 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 15, 15, 15, 15, 29, 29, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 27) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O) `ZINC001735734441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735734441 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ncccc2Cl)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734441 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734441 Building ZINC001735734450 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734450 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/28 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O) `ZINC001735734450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734450 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 14, 14, 35, 35, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 35, 35, 35, 35, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/29 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O) `ZINC001735734450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734450 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 12, 12, 36, 36, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 36, 36, 36, 36, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734450 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 Building ZINC001735734450 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735734450 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 28) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O) `ZINC001735734450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735734450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734450 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 14, 14, 35, 35, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 35, 35, 35, 35, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 29) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O) `ZINC001735734450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735734450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735734450 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 12, 12, 36, 36, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 36, 36, 36, 36, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735734450 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735734450 Building ZINC001735754092 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735754092 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/30 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1) `ZINC001735754092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735754092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735754092 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 22, 25, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/31 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1) `ZINC001735754092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735754092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735754092 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 2, 9, 9, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735754092 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 Building ZINC001735754092 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735754092 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 30) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1) `ZINC001735754092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735754092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735754092 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 22, 25, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 31) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1) `ZINC001735754092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735754092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735754092 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COCC2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 2, 9, 9, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735754092 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735754092 Building ZINC001735756123 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735756123 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/32 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735756123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756123 none CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 50, 50, 38, 50, 38, 38, 12, 12, 12, 12, 6, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/33 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735756123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756123 none CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 50, 50, 30, 50, 30, 30, 9, 9, 9, 9, 4, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 248 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735756123 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 Building ZINC001735756123 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735756123 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 32) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735756123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756123 none CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 50, 50, 38, 50, 38, 38, 12, 12, 12, 12, 6, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 33) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735756123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756123 none CC(C)[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 50, 50, 30, 50, 30, 30, 9, 9, 9, 9, 4, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 248 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735756123 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756123 Building ZINC001735756124 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735756124 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/34 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735756124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756124 none CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 39, 50, 39, 39, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/35 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735756124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756124 none CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 30, 50, 30, 30, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 244 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735756124 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 Building ZINC001735756124 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735756124 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 34) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735756124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756124 none CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 39, 50, 39, 39, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 35) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1) `ZINC001735756124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735756124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735756124 none CC(C)[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 30, 50, 30, 30, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 244 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735756124 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735756124 Building ZINC001735757759 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735757759 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/36 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735757759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757759 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 28, 22, 10, 22, 22, 10, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 22, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/37 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735757759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757759 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 36, 26, 22, 11, 22, 22, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 22, 22, 22, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735757759 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 Building ZINC001735757759 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735757759 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 36) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735757759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757759 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 28, 22, 10, 22, 22, 10, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 22, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 37) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735757759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757759 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 36, 26, 22, 11, 22, 22, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 22, 22, 22, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735757759 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757759 Building ZINC001735757760 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735757760 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/38 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735757760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757760 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 29, 23, 11, 23, 23, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 23, 23, 23, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 231 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/39 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735757760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757760 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 34, 25, 12, 25, 25, 12, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 25, 25, 25, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735757760 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 Building ZINC001735757760 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735757760 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 38) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735757760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757760 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 29, 23, 11, 23, 23, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 23, 23, 23, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 231 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 39) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001735757760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735757760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735757760 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 34, 25, 12, 25, 25, 12, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 25, 25, 25, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735757760 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735757760 Building ZINC001735764717 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735764717 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/40 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1) `ZINC001735764717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735764717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764717 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 5, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 28, 45, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 9, 28, 28, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/41 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1) `ZINC001735764717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735764717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764717 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 23, 46, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 7, 23, 23, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735764717 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 Building ZINC001735764717 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735764717 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 40) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1) `ZINC001735764717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735764717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764717 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 5, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 28, 45, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 9, 28, 28, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 41) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1) `ZINC001735764717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735764717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764717 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 23, 46, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 7, 23, 23, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735764717 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764717 Building ZINC001735764718 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735764718 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/42 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1) `ZINC001735764718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735764718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764718 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 29, 45, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 13, 29, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/43 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1) `ZINC001735764718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735764718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764718 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 4, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 30, 48, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 9, 30, 30, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735764718 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 Building ZINC001735764718 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735764718 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 42) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1) `ZINC001735764718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735764718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764718 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 29, 45, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 13, 29, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 43) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1) `ZINC001735764718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735764718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735764718 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC[C@@H]2CC(C)(C)CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', '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, 12, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 4, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 30, 48, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 9, 30, 30, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735764718 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735764718 Building ZINC001735808596 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735808596 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/44 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735808596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735808596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735808596 none C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 16, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/45 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735808596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735808596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735808596 none C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735808596 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 Building ZINC001735808596 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735808596 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 44) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735808596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735808596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735808596 none C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 16, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 45) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735808596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735808596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735808596 none C[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735808596 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735808596 Building ZINC001735810438 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735810438 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/46 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735810438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735810438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810438 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 35, 47, 50, 50, 50, 50, 50, 50, 50, 16, 5, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/47 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735810438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735810438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810438 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 35, 47, 50, 50, 50, 50, 50, 50, 50, 16, 5, 16, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735810438 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 Building ZINC001735810438 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735810438 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 46) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735810438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735810438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810438 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 35, 47, 50, 50, 50, 50, 50, 50, 50, 16, 5, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 47) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735810438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735810438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810438 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 35, 47, 50, 50, 50, 50, 50, 50, 50, 16, 5, 16, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735810438 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810438 Building ZINC001735810439 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735810439 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/48 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735810439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735810439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810439 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 31, 45, 50, 50, 50, 50, 50, 50, 50, 16, 6, 16, 4, 1, 4, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/49 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735810439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735810439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810439 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 29, 41, 50, 50, 50, 50, 50, 50, 50, 14, 5, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735810439 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 Building ZINC001735810439 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735810439 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 48) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735810439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735810439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810439 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 31, 45, 50, 50, 50, 50, 50, 50, 50, 16, 6, 16, 4, 1, 4, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 49) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735810439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735810439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735810439 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 29, 41, 50, 50, 50, 50, 50, 50, 50, 14, 5, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735810439 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735810439 Building ZINC001735820768 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735820768 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/50 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1) `ZINC001735820768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735820768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735820768 none Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 28, 28, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/51 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1) `ZINC001735820768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735820768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735820768 none Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 28, 28, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735820768 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 Building ZINC001735820768 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735820768 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 50) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1) `ZINC001735820768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735820768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735820768 none Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 28, 28, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 51) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1) `ZINC001735820768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735820768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735820768 none Cc1cc(NC(=O)C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 28, 28, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735820768 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735820768 Building ZINC001735868773 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868773 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/52 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735868773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735868773 none CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 13, 13, 13, 13, 13, 27, 27, 50, 50, 49, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/53 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735868773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735868773 none CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 13, 13, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868773 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 Building ZINC001735868773 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868773 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 52) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735868773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735868773 none CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 13, 13, 13, 13, 13, 27, 27, 50, 50, 49, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 53) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735868773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735868773 none CO[C@@H]1CN(C(=O)c2ccncc2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 13, 13, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868773 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868773 Building ZINC001735868839 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868839 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/54 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1) `ZINC001735868839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735868839 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 13, 10, 13, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 31, 31, 50, 50, 50, 50, 50, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/55 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1) `ZINC001735868839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735868839 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 14, 9, 14, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 9, 30, 30, 50, 50, 50, 50, 50, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868839 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 Building ZINC001735868839 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868839 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 54) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1) `ZINC001735868839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735868839 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 13, 10, 13, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 31, 31, 50, 50, 50, 50, 50, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 55) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1) `ZINC001735868839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735868839 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 14, 9, 14, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 9, 30, 30, 50, 50, 50, 50, 50, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868839 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868839 Building ZINC001735868948 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868948 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/56 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735868948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868948 none CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 9, 14, 14, 31, 36, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 31, 31, 36, 36, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/57 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735868948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868948 none CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 15, 15, 31, 35, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 9, 31, 31, 34, 34, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868948 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 Building ZINC001735868948 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868948 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 56) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735868948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868948 none CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 9, 14, 14, 31, 36, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 31, 31, 36, 36, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 57) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735868948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868948 none CO[C@@H]1CN(C(=O)CC[C@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 15, 15, 31, 35, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 9, 31, 31, 34, 34, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868948 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868948 Building ZINC001735868949 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868949 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/58 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735868949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868949 none CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 14, 14, 31, 37, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 9, 31, 31, 36, 36, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/59 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735868949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868949 none CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 9, 14, 14, 29, 34, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 29, 29, 33, 33, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868949 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 Building ZINC001735868949 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735868949 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 58) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735868949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735868949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868949 none CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 14, 14, 31, 37, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 9, 31, 31, 36, 36, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 59) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735868949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735868949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735868949 none CO[C@@H]1CN(C(=O)CC[C@@H]2CCOC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 9, 14, 14, 29, 34, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 29, 29, 33, 33, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735868949 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735868949 Building ZINC001735869028 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869028 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/60 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735869028 none CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 9, 9, 9, 9, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 53, 54, 23, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/61 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735869028 none CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 9, 9, 9, 9, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 53, 54, 23, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869028 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 Building ZINC001735869028 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869028 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 60) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735869028 none CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 9, 9, 9, 9, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 53, 54, 23, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 61) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735869028 none CO[C@@H]1CN(C(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 9, 9, 9, 9, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 53, 54, 23, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869028 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869028 Building ZINC001735869175 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869175 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/62 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735869175 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/63 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735869175 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 11, 11, 11, 11, 28, 28, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869175 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 Building ZINC001735869175 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869175 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 62) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735869175 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 63) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735869175 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 11, 11, 11, 11, 28, 28, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869175 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869175 Building ZINC001735869360 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869360 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/64 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869360 none CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 6, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 14, 14, 14, 14, 14, 14, 47, 47, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/65 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869360 none CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 6, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 16, 16, 16, 16, 16, 48, 48, 50, 50, 50, 50, 50, 50, 50, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869360 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 Building ZINC001735869360 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869360 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 64) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869360 none CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 6, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 14, 14, 14, 14, 14, 14, 47, 47, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 65) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869360 none CO[C@@H]1CN(C(=O)c2c(C)n[nH]c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 6, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 16, 16, 16, 16, 16, 48, 48, 50, 50, 50, 50, 50, 50, 50, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869360 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869360 Building ZINC001735869382 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869382 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/66 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869382 none CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/67 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869382 none CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869382 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 Building ZINC001735869382 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735869382 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 66) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001735869382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735869382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869382 none CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 67) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001735869382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735869382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735869382 none CO[C@@H]1CN(C(=O)c2cnn(C)c2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735869382 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735869382 Building ZINC001735878259 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735878259 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/68 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1) `ZINC001735878259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735878259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735878259 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 19, 20, 27, 45, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 19, 19, 20, 20, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/69 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1) `ZINC001735878259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735878259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735878259 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 20, 20, 27, 42, 50, 50, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 20, 20, 20, 20, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735878259 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 Building ZINC001735878259 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735878259 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 68) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1) `ZINC001735878259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735878259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735878259 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 19, 20, 27, 45, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 19, 19, 20, 20, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 69) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1) `ZINC001735878259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735878259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735878259 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCOCC1CC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 20, 20, 27, 42, 50, 50, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 20, 20, 20, 20, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735878259 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735878259 Building ZINC001735880769 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735880769 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/70 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F) `ZINC001735880769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735880769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880769 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/71 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F) `ZINC001735880769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735880769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880769 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 22, 22, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735880769 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 Building ZINC001735880769 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735880769 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 70) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F) `ZINC001735880769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735880769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880769 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 71) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F) `ZINC001735880769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735880769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880769 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 22, 22, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735880769 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880769 Building ZINC001735880770 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735880770 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/72 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F) `ZINC001735880770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735880770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880770 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/73 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F) `ZINC001735880770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735880770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880770 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 50, 50, 50, 50, 50, 50, 15, 15, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735880770 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 Building ZINC001735880770 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735880770 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 72) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F) `ZINC001735880770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735880770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880770 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 73) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F) `ZINC001735880770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735880770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001735880770 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](F)C(F)(F)F 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 15, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 50, 50, 50, 50, 50, 50, 15, 15, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735880770 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735880770 Building ZINC001735881644 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735881644 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/74 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1) `ZINC001735881644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735881644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735881644 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 39, 43, 50, 50, 50, 50, 50, 13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 15, 39, 39, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/75 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1) `ZINC001735881644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735881644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735881644 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 31, 41, 50, 50, 50, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 31, 31, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735881644 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 Building ZINC001735881644 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735881644 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 74) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1) `ZINC001735881644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735881644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735881644 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 39, 43, 50, 50, 50, 50, 50, 13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 15, 39, 39, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 75) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1) `ZINC001735881644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735881644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735881644 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cc(C)cn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 31, 41, 50, 50, 50, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 31, 31, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735881644 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735881644 Building ZINC001636448787 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636448787 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/76 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636448787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636448787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001636448787 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 19, 19, 105, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7] 150 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, 40, 41]) total number of confs: 227 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/77 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636448787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636448787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001636448787 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 19, 19, 93, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7] 150 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, 40, 41]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636448787 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 Building ZINC001636448787 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636448787 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 76) grep: /scratch/xiaobo/45881/xch-8058115.60/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: O=C(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636448787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636448787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001636448787 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 19, 19, 105, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7] 150 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, 40, 41]) total number of confs: 227 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 77) grep: /scratch/xiaobo/45881/xch-8058115.60/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: O=C(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636448787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636448787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001636448787 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 19, 19, 93, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7] 150 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, 40, 41]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636448787 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636448787 Building ZINC001735882110 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735882110 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/78 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1) `ZINC001735882110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735882110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735882110 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 25, 23, 41, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 25, 25, 31, 31, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/79 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1) `ZINC001735882110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735882110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735882110 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 28, 24, 42, 50, 50, 50, 50, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 28, 28, 35, 35, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735882110 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 Building ZINC001735882110 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735882110 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 78) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1) `ZINC001735882110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735882110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735882110 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 25, 23, 41, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 25, 25, 31, 31, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 79) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1) `ZINC001735882110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735882110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735882110 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCN1CCCC1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 28, 24, 42, 50, 50, 50, 50, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 28, 28, 35, 35, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735882110 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735882110 Building ZINC001735886327 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735886327 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/80 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001735886327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735886327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886327 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 30, 34, 19, 18, 5, 5, 5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 34, 29, 27, 23, 23, 18, 18, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/81 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001735886327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735886327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886327 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 28, 31, 22, 22, 7, 7, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 50, 31, 26, 26, 26, 26, 22, 22, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735886327 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 Building ZINC001735886327 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735886327 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 80) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001735886327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735886327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886327 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 30, 34, 19, 18, 5, 5, 5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 34, 29, 27, 23, 23, 18, 18, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 81) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001735886327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735886327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886327 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 28, 31, 22, 22, 7, 7, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 50, 31, 26, 26, 26, 26, 22, 22, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735886327 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886327 Building ZINC001735886820 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735886820 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/82 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C) `ZINC001735886820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735886820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886820 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 20, 38, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 27, 27, 33, 34, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/83 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C) `ZINC001735886820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735886820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886820 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 17, 36, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735886820 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 Building ZINC001735886820 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735886820 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 82) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C) `ZINC001735886820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735886820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886820 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 20, 38, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 27, 27, 33, 34, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 83) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C) `ZINC001735886820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735886820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735886820 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(=O)N(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 17, 36, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735886820 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735886820 Building ZINC001735888195 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735888195 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/84 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C) `ZINC001735888195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735888195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735888195 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 22, 26, 47, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 26, 26, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/85 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C) `ZINC001735888195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735888195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735888195 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 19, 31, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 24, 24, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735888195 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 Building ZINC001735888195 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735888195 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 84) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C) `ZINC001735888195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735888195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735888195 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 22, 26, 47, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 26, 26, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 85) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C) `ZINC001735888195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735888195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735888195 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCN(C)C 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 19, 31, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 24, 24, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735888195 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888195 Building ZINC001735888551 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735888551 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/86 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1) `ZINC001735888551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735888551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735888551 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 21, 27, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 21, 21, 27, 27, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/87 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1) `ZINC001735888551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735888551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735888551 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 26, 30, 50, 50, 50, 50, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 26, 26, 30, 30, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735888551 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 Building ZINC001735888551 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735888551 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 86) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1) `ZINC001735888551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735888551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735888551 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 21, 27, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 21, 21, 27, 27, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 87) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1) `ZINC001735888551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735888551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735888551 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1ccnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 26, 30, 50, 50, 50, 50, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 26, 26, 30, 30, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735888551 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735888551 Building ZINC001735892985 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735892985 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/88 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1) `ZINC001735892985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735892985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735892985 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 42, 50, 50, 50, 46, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/89 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1) `ZINC001735892985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735892985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735892985 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 4, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 23, 23, 23, 45, 50, 50, 50, 50, 50, 50, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 23, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735892985 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 Building ZINC001735892985 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735892985 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 88) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1) `ZINC001735892985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735892985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735892985 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 42, 50, 50, 50, 46, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 89) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1) `ZINC001735892985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735892985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735892985 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ncccn1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 4, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 23, 23, 23, 45, 50, 50, 50, 50, 50, 50, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 23, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735892985 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735892985 Building ZINC001735911321 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911321 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/90 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O) `ZINC001735911321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735911321 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 23, 23, 49, 49, 49, 49, 49, 50, 50, 49, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 49, 49, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/91 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O) `ZINC001735911321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735911321 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 23, 23, 49, 49, 49, 49, 49, 50, 50, 49, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 49, 49, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911321 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 Building ZINC001735911321 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911321 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 90) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O) `ZINC001735911321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735911321 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 23, 23, 49, 49, 49, 49, 49, 50, 50, 49, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 49, 49, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 91) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O) `ZINC001735911321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735911321 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2c2ccncc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 23, 23, 49, 49, 49, 49, 49, 50, 50, 49, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 49, 49, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911321 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911321 Building ZINC001735911424 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911424 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/92 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C) `ZINC001735911424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911424 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 20, 10, 20, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/93 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C) `ZINC001735911424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911424 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 20, 9, 20, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911424 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 Building ZINC001735911424 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911424 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 92) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C) `ZINC001735911424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911424 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 20, 10, 20, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 93) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C) `ZINC001735911424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911424 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 20, 9, 20, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911424 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911424 Building ZINC001735911427 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911427 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/94 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735911427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911427 none Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 30, 28, 11, 10, 11, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 30, 30, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/95 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735911427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911427 none Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 32, 13, 10, 13, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 34, 34, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911427 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 Building ZINC001735911427 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911427 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 94) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735911427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911427 none Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 30, 28, 11, 10, 11, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 30, 30, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 95) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735911427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911427 none Cc1cncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 32, 13, 10, 13, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 34, 34, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911427 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911427 Building ZINC001735911445 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911445 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/96 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O) `ZINC001735911445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735911445 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 7, 7, 7, 24, 34, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 24, 24, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 161 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/97 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O) `ZINC001735911445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735911445 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 20, 31, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 20, 20, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911445 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 Building ZINC001735911445 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911445 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 96) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O) `ZINC001735911445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735911445 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 7, 7, 7, 24, 34, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 24, 24, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 161 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 97) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O) `ZINC001735911445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735911445 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccsc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 20, 31, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 20, 20, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911445 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911445 Building ZINC001735911572 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911572 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/98 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O) `ZINC001735911572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735911572 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 22, 25, 32, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 22, 22, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 219 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/99 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O) `ZINC001735911572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735911572 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 19, 23, 34, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 19, 19, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911572 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 Building ZINC001735911572 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911572 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 98) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O) `ZINC001735911572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735911572 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 22, 25, 32, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 22, 22, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 219 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 99) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O) `ZINC001735911572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735911572 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 19, 23, 34, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 19, 19, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911572 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911572 Building ZINC001735911770 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911770 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/100 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1) `ZINC001735911770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911770 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 39, 39, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 39, 39, 39, 39, 50, 50, 50, 50, 50, 39, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 39, 39, 39] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/101 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1) `ZINC001735911770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911770 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 19, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35, 35] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911770 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 Building ZINC001735911770 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911770 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 100) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1) `ZINC001735911770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911770 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 39, 39, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 39, 39, 39, 39, 50, 50, 50, 50, 50, 39, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 39, 39, 39] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 101) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1) `ZINC001735911770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735911770 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 19, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35, 35] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911770 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911770 Building ZINC001735911933 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911933 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/102 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O) `ZINC001735911933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735911933 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 34, 50, 50, 47, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 34, 34, 48, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 257 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/103 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O) `ZINC001735911933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735911933 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 10, 10, 30, 50, 50, 48, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 48, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911933 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 Building ZINC001735911933 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911933 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 102) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O) `ZINC001735911933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735911933 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 34, 50, 50, 47, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 34, 34, 48, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 257 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 103) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O) `ZINC001735911933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001735911933 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 10, 10, 30, 50, 50, 48, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 48, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911933 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911933 Building ZINC001735911934 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911934 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/104 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C) `ZINC001735911934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911934 none Cc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/105 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C) `ZINC001735911934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911934 none Cc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911934 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 Building ZINC001735911934 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735911934 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 104) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C) `ZINC001735911934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735911934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911934 none Cc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 105) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C) `ZINC001735911934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735911934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735911934 none Cc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735911934 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735911934 Building ZINC001735912033 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912033 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/106 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912033 none COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 50, 38, 14, 38, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/107 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912033 none COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 50, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912033 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 Building ZINC001735912033 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912033 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 106) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912033 none COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 50, 38, 14, 38, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 107) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912033 none COc1cccc(F)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 50, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912033 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912033 Building ZINC001735912064 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912064 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/108 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O) `ZINC001735912064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735912064 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 9, 9, 26, 28, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 28, 28, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/109 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O) `ZINC001735912064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735912064 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 10, 10, 28, 34, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 28, 34, 34, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912064 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 Building ZINC001735912064 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912064 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 108) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O) `ZINC001735912064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735912064 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 9, 9, 26, 28, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 28, 28, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 109) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O) `ZINC001735912064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001735912064 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cscn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 14, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 10, 10, 28, 34, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 28, 34, 34, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912064 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912064 Building ZINC001735912082 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912082 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/110 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912082 none Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 33, 29, 13, 9, 13, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/111 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912082 none Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 28, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912082 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 Building ZINC001735912082 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912082 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 110) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912082 none Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 33, 29, 13, 9, 13, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 111) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912082 none Cc1cc(C)n(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 28, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912082 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912082 Building ZINC001735912151 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912151 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/112 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912151 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [50, 48, 48, 48, 48, 48, 48, 48, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/113 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912151 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [50, 48, 48, 48, 48, 48, 48, 48, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912151 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 Building ZINC001735912151 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912151 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 112) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912151 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [50, 48, 48, 48, 48, 48, 48, 48, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 113) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912151 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [50, 48, 48, 48, 48, 48, 48, 48, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912151 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912151 Building ZINC001735912161 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912161 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/114 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001735912161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912161 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 23, 10, 23, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 50, 50, 50, 50, 50, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 31, 31, 31] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/115 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001735912161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912161 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 20, 9, 20, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 31, 50, 50, 50, 50, 50, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 31, 31, 31] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912161 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 Building ZINC001735912161 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912161 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 114) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001735912161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912161 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 23, 10, 23, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 50, 50, 50, 50, 50, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 31, 31, 31] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 115) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001735912161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912161 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 20, 9, 20, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 31, 50, 50, 50, 50, 50, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 31, 31, 31] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912161 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912161 Building ZINC001735912544 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912544 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/116 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O) `ZINC001735912544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912544 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 20, 43, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 20, 20, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/117 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O) `ZINC001735912544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912544 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 18, 40, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 18, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912544 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 Building ZINC001735912544 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912544 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 116) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O) `ZINC001735912544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912544 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 20, 43, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 20, 20, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 117) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O) `ZINC001735912544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912544 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2ccccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 18, 40, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 18, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912544 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912544 Building ZINC001735912554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/118 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/119 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/120 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/120' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/121 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/121' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 Building ZINC001735912554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 118) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 119) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 120) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 121) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 Building ZINC001735912554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 118) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 119) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 120) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 121) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 Building ZINC001735912554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 118) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 119) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 120) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 121) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912554 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912554 Building ZINC001735912555 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912555 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/122 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/123 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/124 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/124' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/125 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/125' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912555 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 Building ZINC001735912555 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912555 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 122) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 123) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 124) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 125) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912555 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 Building ZINC001735912555 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912555 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 122) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 123) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 124) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 125) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912555 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 Building ZINC001735912555 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912555 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 122) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 123) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 24, 14, 24, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 215 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 124) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 125) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001735912555 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 23, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912555 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912555 Building ZINC001735912556 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912556 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/126 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912556 none CC(C)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 21, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 49, 49, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/127 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912556 none CC(C)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 49, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912556 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 Building ZINC001735912556 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912556 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 126) grep: /scratch/xiaobo/45881/xch-8058115.60/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)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912556 none CC(C)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 21, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 49, 49, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 127) grep: /scratch/xiaobo/45881/xch-8058115.60/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)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912556 none CC(C)n1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 49, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912556 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912556 Building ZINC001735912559 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912559 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/128 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O) `ZINC001735912559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735912559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 17, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/129 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O) `ZINC001735912559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735912559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912559 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 Building ZINC001735912559 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912559 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 128) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O) `ZINC001735912559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735912559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 17, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 129) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O) `ZINC001735912559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735912559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3c2OCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912559 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912559 Building ZINC001735912577 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912577 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/130 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912577 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 21, 9, 21, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/131 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912577 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 50, 50, 45, 45, 45, 45, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912577 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 Building ZINC001735912577 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912577 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 130) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912577 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 21, 9, 21, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 131) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912577 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 50, 50, 45, 45, 45, 45, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912577 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912577 Building ZINC001735912578 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912578 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/132 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912578 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 50, 50, 44, 44, 44, 44, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/133 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912578 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 50, 50, 45, 45, 45, 45, 21, 10, 21, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912578 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 Building ZINC001735912578 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912578 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 132) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912578 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 50, 50, 44, 44, 44, 44, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 133) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912578 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 50, 50, 45, 45, 45, 45, 21, 10, 21, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912578 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912578 Building ZINC001735912716 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912716 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/134 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912716 none CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 48, 50, 50, 50, 50, 50, 50, 50, 48, 48, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/135 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912716 none CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 24, 10, 24, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 50, 50, 50, 50, 50, 50, 50, 49, 49, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912716 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 Building ZINC001735912716 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912716 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 134) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912716 none CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 48, 50, 50, 50, 50, 50, 50, 50, 48, 48, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 135) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001735912716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001735912716 none CC(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 24, 10, 24, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 50, 50, 50, 50, 50, 50, 50, 49, 49, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912716 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912716 Building ZINC001735912722 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912722 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/136 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912722 none CC(C)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/137 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912722 none CC(C)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912722 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 Building ZINC001735912722 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912722 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 136) grep: /scratch/xiaobo/45881/xch-8058115.60/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)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912722 none CC(C)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 137) grep: /scratch/xiaobo/45881/xch-8058115.60/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)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001735912722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912722 none CC(C)c1nnsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [50, 50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912722 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912722 Building ZINC001735912762 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912762 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/138 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/139 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/140 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/140' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/141 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/141' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912762 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 Building ZINC001735912762 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912762 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 138) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 139) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 140) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 141) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912762 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 Building ZINC001735912762 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912762 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 138) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 139) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 140) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 141) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912762 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 Building ZINC001735912762 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001735912762 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 138) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 139) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 140) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 141) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O) `ZINC001735912762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001735912762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001735912762 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 10, 10, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912762 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912762 Building ZINC001735912771 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912771 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/142 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912771 none CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 32, 20, 9, 20, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 32, 32, 32] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/143 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912771 none CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 32, 20, 9, 20, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 32, 32, 32] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912771 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 Building ZINC001735912771 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912771 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 142) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912771 none CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 32, 20, 9, 20, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 32, 32, 32] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 143) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912771 none CCn1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 32, 20, 9, 20, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 32, 32, 32] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912771 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912771 Building ZINC001735912793 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912793 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/144 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912793 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 21, 41, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 21, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/145 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912793 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 22, 36, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 22, 22, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 193 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912793 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 Building ZINC001735912793 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912793 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 144) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912793 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 21, 41, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 21, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 145) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912793 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 22, 36, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 22, 22, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 193 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912793 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912793 Building ZINC001735912794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/146 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912794 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 24, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 24, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/147 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912794 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 21, 37, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 21, 21, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 192 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 Building ZINC001735912794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 146) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912794 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 24, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 24, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 147) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001735912794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001735912794 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 21, 37, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 21, 21, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 192 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912794 Building ZINC001735912806 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912806 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/148 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O) `ZINC001735912806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912806 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/149 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O) `ZINC001735912806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912806 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912806 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 Building ZINC001735912806 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912806 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 148) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O) `ZINC001735912806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912806 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 149) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O) `ZINC001735912806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912806 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn3ccccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912806 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912806 Building ZINC001735912808 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912808 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/150 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O) `ZINC001735912808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001735912808 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 25, 25, 49, 49, 49, 49, 50, 50, 49, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 49, 49, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/151 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O) `ZINC001735912808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001735912808 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 47, 47, 47, 47, 50, 50, 47, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 47, 47, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912808 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 Building ZINC001735912808 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912808 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 150) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O) `ZINC001735912808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001735912808 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 25, 25, 49, 49, 49, 49, 50, 50, 49, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 49, 49, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 151) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O) `ZINC001735912808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001735912808 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 47, 47, 47, 47, 50, 50, 47, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 47, 47, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912808 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912808 Building ZINC001735912955 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912955 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/152 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912955 none CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 29, 29, 29, 29, 15, 9, 15, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 29, 29, 29] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/153 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912955 none CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 31, 31, 31] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912955 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 Building ZINC001735912955 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912955 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 152) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912955 none CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 29, 29, 29, 29, 15, 9, 15, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 29, 29, 29] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 153) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001735912955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735912955 none CCCn1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 31, 31, 31] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912955 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912955 Building ZINC001735912978 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912978 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/154 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735912978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912978 none COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 28, 13, 9, 13, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 50, 50, 50, 50, 50, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 28] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/155 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735912978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912978 none COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 23, 23, 23, 23, 9, 6, 9, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 23, 50, 50, 50, 50, 50, 23, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 23] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912978 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 Building ZINC001735912978 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912978 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 154) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735912978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912978 none COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 28, 13, 9, 13, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 50, 50, 50, 50, 50, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 28] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 155) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001735912978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735912978 none COCc1csc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 23, 23, 23, 23, 9, 6, 9, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 23, 50, 50, 50, 50, 50, 23, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 23] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912978 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912978 Building ZINC001735912996 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912996 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/156 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O) `ZINC001735912996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912996 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 4, 4, 4, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 23, 23, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/157 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O) `ZINC001735912996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912996 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 5, 5, 5, 5, 6, 6, 27, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 27, 27, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912996 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 Building ZINC001735912996 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912996 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 156) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O) `ZINC001735912996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912996 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 4, 4, 4, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 23, 23, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 157) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O) `ZINC001735912996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001735912996 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2cc(F)ccc2F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 5, 5, 5, 5, 6, 6, 27, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 27, 27, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912996 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912996 Building ZINC001735912999 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912999 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/158 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O) `ZINC001735912999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735912999 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 19, 19, 19, 19, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 57] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/159 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O) `ZINC001735912999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735912999 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 15, 15, 15, 15, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912999 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 Building ZINC001735912999 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735912999 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 158) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O) `ZINC001735912999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735912999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735912999 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 19, 19, 19, 19, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 57] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 159) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O) `ZINC001735912999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735912999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735912999 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3n(c2)CCCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 15, 15, 15, 15, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735912999 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735912999 Building ZINC001735913000 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913000 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/160 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O) `ZINC001735913000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913000 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/161 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O) `ZINC001735913000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913000 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913000 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 Building ZINC001735913000 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913000 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 160) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O) `ZINC001735913000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913000 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 161) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O) `ZINC001735913000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913000 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913000 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913000 Building ZINC001735913012 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913012 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/162 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1) `ZINC001735913012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735913012 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 33, 19, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/163 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1) `ZINC001735913012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735913012 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 33, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 33, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913012 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 Building ZINC001735913012 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913012 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 162) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1) `ZINC001735913012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735913012 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 33, 19, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 163) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1) `ZINC001735913012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001735913012 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 33, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 33, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913012 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913012 Building ZINC001735913137 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913137 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/164 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001735913137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735913137 none CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 13, 32, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/165 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001735913137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735913137 none CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 27, 14, 27, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913137 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 Building ZINC001735913137 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913137 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 164) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001735913137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735913137 none CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 13, 32, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 165) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001735913137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735913137 none CC(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 27, 14, 27, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913137 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913137 Building ZINC001735913194 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913194 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/166 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O) `ZINC001735913194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913194 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/167 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O) `ZINC001735913194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913194 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 9, 9, 9, 9, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913194 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 Building ZINC001735913194 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913194 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 166) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O) `ZINC001735913194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913194 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 167) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O) `ZINC001735913194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001735913194 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nccc3cccnc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 9, 9, 9, 9, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913194 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913194 Building ZINC001735913217 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913217 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/168 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O) `ZINC001735913217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735913217 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/169 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O) `ZINC001735913217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735913217 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913217 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 Building ZINC001735913217 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735913217 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 168) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O) `ZINC001735913217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735913217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735913217 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 169) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O) `ZINC001735913217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735913217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001735913217 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(C(F)F)ncn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735913217 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735913217 Building ZINC001735925412 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735925412 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/170 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1) `ZINC001735925412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735925412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735925412 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 21, 19, 4, 4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 27, 29, 27, 27, 19, 19, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/171 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1) `ZINC001735925412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735925412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735925412 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 22, 21, 4, 4, 4, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 32, 35, 27, 27, 21, 21, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735925412 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 Building ZINC001735925412 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735925412 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 170) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1) `ZINC001735925412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735925412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735925412 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 21, 19, 4, 4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 27, 29, 27, 27, 19, 19, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 171) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1) `ZINC001735925412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735925412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001735925412 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 22, 21, 4, 4, 4, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 32, 35, 27, 27, 21, 21, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735925412 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735925412 Building ZINC001735934910 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735934910 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/172 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735934910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735934910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735934910 none CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 35, 30, 27, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 47, 47, 35, 35, 35, 35, 35, 35, 27, 27, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/173 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735934910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735934910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735934910 none CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 37, 33, 30, 6, 6, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 37, 37, 37, 37, 37, 37, 30, 30, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735934910 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 Building ZINC001735934910 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735934910 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 172) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735934910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735934910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735934910 none CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 35, 30, 27, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 47, 47, 35, 35, 35, 35, 35, 35, 27, 27, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 173) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735934910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735934910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735934910 none CCOCCCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 37, 33, 30, 6, 6, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 37, 37, 37, 37, 37, 37, 30, 30, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735934910 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735934910 Building ZINC001735940408 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735940408 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/174 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735940408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735940408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735940408 none Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 21, 25, 5, 5, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 31, 31, 31, 31, 25, 25, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/175 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735940408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735940408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735940408 none Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 22, 25, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 31, 31, 31, 31, 25, 25, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735940408 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 Building ZINC001735940408 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735940408 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 174) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735940408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735940408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735940408 none Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 21, 25, 5, 5, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 31, 31, 31, 31, 25, 25, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 175) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735940408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735940408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735940408 none Cc1nccn1CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 22, 25, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 31, 31, 31, 31, 25, 25, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735940408 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735940408 Building ZINC001735947234 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735947234 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/176 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735947234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735947234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735947234 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 45, 40, 20, 17, 14, 9, 9, 9, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 45, 45, 40, 40, 20, 20, 14, 14, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/177 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735947234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735947234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735947234 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 45, 40, 18, 16, 13, 7, 7, 7, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 45, 45, 40, 40, 18, 18, 13, 13, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735947234 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 Building ZINC001735947234 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735947234 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 176) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735947234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735947234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735947234 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 45, 40, 20, 17, 14, 9, 9, 9, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 45, 45, 40, 40, 20, 20, 14, 14, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 177) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001735947234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735947234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735947234 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 45, 40, 18, 16, 13, 7, 7, 7, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 45, 45, 40, 40, 18, 18, 13, 13, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735947234 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735947234 Building ZINC001636517991 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636517991 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/178 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O) `ZINC001636517991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636517991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001636517991 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', '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, 1, 1, 16, 14, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 40, 29, 29, 29, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 40, 40, 29, 14, 14, 3, 3, 3, 87] 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]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/179 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O) `ZINC001636517991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636517991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001636517991 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', '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, 1, 1, 16, 14, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 40, 30, 30, 30, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 49, 49, 49, 49, 49, 40, 40, 30, 14, 14, 3, 3, 3, 90] 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]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636517991 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 Building ZINC001636517991 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636517991 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 178) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O) `ZINC001636517991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636517991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001636517991 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', '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, 1, 1, 16, 14, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 40, 29, 29, 29, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 40, 40, 29, 14, 14, 3, 3, 3, 87] 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]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 179) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O) `ZINC001636517991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636517991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001636517991 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', '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, 1, 1, 16, 14, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 40, 30, 30, 30, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 49, 49, 49, 49, 49, 40, 40, 30, 14, 14, 3, 3, 3, 90] 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]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636517991 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636517991 Building ZINC001735969706 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735969706 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/180 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21) `ZINC001735969706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735969706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969706 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 17, 28, 28, 28, 40, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 17, 17, 28, 40, 40, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 211 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/181 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21) `ZINC001735969706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735969706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969706 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 31, 31, 31, 45, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 23, 23, 31, 45, 45, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 204 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735969706 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 Building ZINC001735969706 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735969706 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 180) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21) `ZINC001735969706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735969706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969706 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 17, 28, 28, 28, 40, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 17, 17, 28, 40, 40, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 211 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 181) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21) `ZINC001735969706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735969706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969706 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CC(=O)NCC3CC3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 31, 31, 31, 45, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 23, 23, 31, 45, 45, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 204 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735969706 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969706 Building ZINC001735969880 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735969880 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/182 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1) `ZINC001735969880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969880 none CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 38, 20, 38, 20, 20, 20, 20, 20, 20, 14, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 41, 41, 41, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/183 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1) `ZINC001735969880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969880 none CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 39, 19, 39, 19, 19, 19, 19, 19, 19, 14, 1, 14, 1, 1, 1, 1, 1, 1, 19, 19, 19, 42, 42, 42, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735969880 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 Building ZINC001735969880 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735969880 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 182) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1) `ZINC001735969880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969880 none CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 38, 20, 38, 20, 20, 20, 20, 20, 20, 14, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 41, 41, 41, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 183) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1) `ZINC001735969880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001735969880 none CNC(=O)C1(C(=O)N2CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]3C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 39, 19, 39, 19, 19, 19, 19, 19, 19, 14, 1, 14, 1, 1, 1, 1, 1, 1, 19, 19, 19, 42, 42, 42, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735969880 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735969880 Building ZINC001735970251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735970251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/184 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21) `ZINC001735970251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735970251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735970251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 7, 8, 8, 8, 8, 8, 8, 8, 13, 13, 28, 28, 37, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 33, 33, 36, 36, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/185 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21) `ZINC001735970251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735970251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735970251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 7, 8, 8, 8, 8, 8, 8, 8, 14, 14, 22, 26, 39, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 28, 28, 38, 38, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735970251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 Building ZINC001735970251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735970251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 184) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21) `ZINC001735970251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735970251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735970251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 7, 8, 8, 8, 8, 8, 8, 8, 13, 13, 28, 28, 37, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 33, 33, 36, 36, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 185) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21) `ZINC001735970251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735970251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001735970251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCn3ccnn3)C[C@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 7, 8, 8, 8, 8, 8, 8, 8, 14, 14, 22, 26, 39, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 28, 28, 38, 38, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735970251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735970251 Building ZINC001735972324 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735972324 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/186 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001735972324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735972324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735972324 none CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 28, 17, 28, 17, 17, 17, 17, 17, 17, 14, 2, 14, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 166 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/187 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001735972324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735972324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735972324 none CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 23, 18, 23, 18, 18, 18, 18, 18, 18, 13, 2, 13, 1, 1, 1, 1, 1, 1, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735972324 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 Building ZINC001735972324 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735972324 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 186) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001735972324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735972324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735972324 none CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 28, 17, 28, 17, 17, 17, 17, 17, 17, 14, 2, 14, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 166 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 187) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001735972324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735972324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001735972324 none CC(C)(C)C(=O)NCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 23, 18, 23, 18, 18, 18, 18, 18, 18, 13, 2, 13, 1, 1, 1, 1, 1, 1, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735972324 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735972324 Building ZINC001735997386 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735997386 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/188 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001735997386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735997386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735997386 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 23, 26, 28, 41, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 23, 23, 26, 26, 28, 28, 41, 41, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/189 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001735997386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735997386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735997386 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 17, 22, 24, 40, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 17, 17, 22, 22, 24, 24, 40, 40, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735997386 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 Building ZINC001735997386 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001735997386 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 188) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001735997386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001735997386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735997386 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 23, 26, 28, 41, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 23, 23, 26, 26, 28, 28, 41, 41, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 189) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001735997386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001735997386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001735997386 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2CN(C(=O)CCCCC(N)=O)[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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 17, 22, 24, 40, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 17, 17, 22, 22, 24, 24, 40, 40, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001735997386 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001735997386 Building ZINC001736002396 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736002396 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/190 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1) `ZINC001736002396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736002396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736002396 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 27, 38, 38, 38, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 8, 27, 27, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/191 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1) `ZINC001736002396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736002396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736002396 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 26, 40, 40, 40, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 26, 26, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736002396 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 Building ZINC001736002396 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736002396 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 190) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1) `ZINC001736002396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736002396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736002396 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 27, 38, 38, 38, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 8, 27, 27, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 191) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1) `ZINC001736002396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736002396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736002396 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 26, 40, 40, 40, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 26, 26, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736002396 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736002396 Building ZINC001736006794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736006794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/192 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O) `ZINC001736006794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736006794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736006794 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 14, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/193 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O) `ZINC001736006794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736006794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736006794 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 15, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736006794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 Building ZINC001736006794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736006794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 192) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O) `ZINC001736006794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736006794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736006794 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 14, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 193) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O) `ZINC001736006794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736006794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736006794 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1CCOCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 15, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736006794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006794 Building ZINC001736006855 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736006855 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/194 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001736006855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736006855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736006855 none Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 22, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/195 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001736006855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736006855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736006855 none Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 27, 13, 13, 13, 13, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736006855 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 Building ZINC001736006855 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736006855 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 194) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001736006855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736006855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736006855 none Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 22, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 195) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001736006855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736006855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736006855 none Cn1nc(C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 27, 13, 13, 13, 13, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736006855 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006855 Building ZINC001736006881 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736006881 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/196 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001736006881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736006881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736006881 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 20, 22, 24, 39, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 6, 20, 20, 24, 24, 24, 24, 39, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/197 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001736006881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736006881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736006881 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 24, 29, 33, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 31, 31, 33, 33, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736006881 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 Building ZINC001736006881 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736006881 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 196) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001736006881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736006881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736006881 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 20, 22, 24, 39, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 6, 20, 20, 24, 24, 24, 24, 39, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 197) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001736006881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736006881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736006881 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 24, 29, 33, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 31, 31, 33, 33, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736006881 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736006881 Building ZINC001736007366 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007366 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/198 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1) `ZINC001736007366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007366 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 25, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/199 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1) `ZINC001736007366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007366 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 28, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 28, 28, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007366 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 Building ZINC001736007366 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007366 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 198) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1) `ZINC001736007366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007366 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 25, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 199) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1) `ZINC001736007366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007366 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 28, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 28, 28, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007366 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007366 Building ZINC001736007367 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007367 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/200 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1) `ZINC001736007367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007367 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 24, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 24, 24, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/201 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1) `ZINC001736007367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007367 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 31, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 8, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007367 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 Building ZINC001736007367 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007367 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 200) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1) `ZINC001736007367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007367 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 24, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 24, 24, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 201) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1) `ZINC001736007367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736007367 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CO[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 31, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 8, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007367 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007367 Building ZINC001736007591 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007591 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/202 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007591 none CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 50, 17, 17, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 17, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/203 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007591 none CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 50, 15, 15, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007591 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 Building ZINC001736007591 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007591 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 202) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007591 none CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 50, 17, 17, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 17, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 203) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007591 none CN1C[C@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 50, 15, 15, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007591 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007591 Building ZINC001736007592 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007592 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/204 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007592 none CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 50, 17, 17, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 17, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/205 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007592 none CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 50, 19, 19, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 19, 8, 8, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007592 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 Building ZINC001736007592 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007592 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 204) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007592 none CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 50, 17, 17, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 17, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 205) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001736007592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007592 none CN1C[C@@H](C(=O)N[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 50, 19, 19, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 19, 8, 8, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007592 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007592 Building ZINC001736007608 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007608 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/206 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007608 none C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 45, 21, 21, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 45, 45, 45, 21, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/207 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007608 none C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 21, 43, 21, 21, 12, 12, 12, 12, 12, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 43, 43, 43, 21, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007608 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 Building ZINC001736007608 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007608 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 206) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007608 none C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 45, 21, 21, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 45, 45, 45, 21, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 207) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007608 none C[C@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 21, 43, 21, 21, 12, 12, 12, 12, 12, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 43, 43, 43, 21, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007608 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007608 Building ZINC001736007609 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007609 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/208 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007609 none C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 48, 22, 22, 11, 11, 11, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 48, 48, 48, 22, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/209 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007609 none C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 47, 25, 25, 15, 15, 15, 15, 15, 15, 15, 3, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 47, 47, 47, 25, 15, 15, 15, 15, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007609 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 Building ZINC001736007609 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007609 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 208) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007609 none C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 48, 22, 22, 11, 11, 11, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 48, 48, 48, 22, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 209) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O) `ZINC001736007609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736007609 none C[C@@H](C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 47, 25, 25, 15, 15, 15, 15, 15, 15, 15, 3, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 47, 47, 47, 25, 15, 15, 15, 15, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007609 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007609 Building ZINC001736007794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/210 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736007794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007794 none CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 50, 19, 19, 11, 11, 11, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 19, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/211 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736007794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007794 none CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 50, 22, 22, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 Building ZINC001736007794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 210) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736007794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007794 none CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 50, 19, 19, 11, 11, 11, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 19, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 211) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736007794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736007794 none CN1C(=O)CC[C@H]1C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 50, 22, 22, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007794 Building ZINC001736007811 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007811 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/212 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1) `ZINC001736007811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736007811 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 25, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/213 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1) `ZINC001736007811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736007811 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 26, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 18, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007811 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 Building ZINC001736007811 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007811 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 212) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1) `ZINC001736007811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736007811 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 25, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 213) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1) `ZINC001736007811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736007811 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 26, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 18, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007811 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007811 Building ZINC001736007824 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007824 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/214 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CCC1=O) `ZINC001736007824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736007824 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 13, 13, 21, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/215 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CCC1=O) `ZINC001736007824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736007824 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 16, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007824 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 Building ZINC001736007824 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736007824 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 214) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CCC1=O) `ZINC001736007824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736007824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736007824 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 13, 13, 21, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 215) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CCC1=O) `ZINC001736007824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736007824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736007824 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 16, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736007824 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736007824 Building ZINC001736008010 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736008010 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/216 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736008010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736008010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736008010 none CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 25, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 9, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 57, 55, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/217 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736008010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736008010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736008010 none CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 23, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 7, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 57, 55, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736008010 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 Building ZINC001736008010 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736008010 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 216) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736008010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736008010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736008010 none CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 25, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 9, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 57, 55, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 217) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736008010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736008010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736008010 none CN(C)CCOCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 23, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 7, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 57, 55, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736008010 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008010 Building ZINC001736008032 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736008032 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/218 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O) `ZINC001736008032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736008032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736008032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens 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, 3, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 11, 36, 36, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 311 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/219 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O) `ZINC001736008032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736008032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736008032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 8, 40, 40, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 316 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736008032 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 Building ZINC001736008032 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736008032 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 218) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O) `ZINC001736008032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736008032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736008032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens 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, 3, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 11, 36, 36, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 311 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 219) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O) `ZINC001736008032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736008032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736008032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)Cn1cnnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 8, 40, 40, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 316 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736008032 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008032 Building ZINC001736008349 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736008349 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/220 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1) `ZINC001736008349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736008349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736008349 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 41, 41, 41, 41, 41, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 15, 41, 50, 50, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/221 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1) `ZINC001736008349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736008349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736008349 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 41, 41, 41, 41, 41, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 9, 9, 9, 16, 41, 50, 50, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736008349 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 Building ZINC001736008349 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736008349 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 220) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1) `ZINC001736008349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736008349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736008349 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 41, 41, 41, 41, 41, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 15, 41, 50, 50, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 221) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1) `ZINC001736008349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736008349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736008349 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1c[nH]c(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 41, 41, 41, 41, 41, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 9, 9, 9, 16, 41, 50, 50, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736008349 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736008349 Building ZINC001636577070 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636577070 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/222 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636577070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577070 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 9, 18, 18, 18, 26, 26, 26, 26, 26, 2, 2, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 9, 9, 18, 26, 26, 26, 26, 26, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/223 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636577070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577070 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 13, 13, 13, 26, 26, 26, 26, 26, 3, 3, 10, 10, 10, 10, 10, 3, 2, 2, 2, 2, 2, 2, 6, 6, 13, 26, 26, 26, 26, 26, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636577070 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 Building ZINC001636577070 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636577070 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 222) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636577070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577070 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 9, 18, 18, 18, 26, 26, 26, 26, 26, 2, 2, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 9, 9, 18, 26, 26, 26, 26, 26, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 223) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636577070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577070 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 13, 13, 13, 26, 26, 26, 26, 26, 3, 3, 10, 10, 10, 10, 10, 3, 2, 2, 2, 2, 2, 2, 6, 6, 13, 26, 26, 26, 26, 26, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636577070 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577070 Building ZINC001636577071 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636577071 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/224 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636577071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577071 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 27, 27, 27, 27, 27, 3, 3, 10, 10, 10, 10, 10, 3, 2, 2, 2, 2, 2, 2, 6, 6, 14, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/225 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636577071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577071 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 8, 14, 14, 14, 24, 24, 24, 24, 24, 2, 2, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 24, 24, 24, 24, 24, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636577071 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 Building ZINC001636577071 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636577071 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 224) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636577071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577071 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 27, 27, 27, 27, 27, 3, 3, 10, 10, 10, 10, 10, 3, 2, 2, 2, 2, 2, 2, 6, 6, 14, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 225) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(C)c2)cn1) `ZINC001636577071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636577071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001636577071 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2CNC(=O)c2cnn(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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 8, 14, 14, 14, 24, 24, 24, 24, 24, 2, 2, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 24, 24, 24, 24, 24, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636577071 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636577071 Building ZINC001736085075 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736085075 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/226 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1) `ZINC001736085075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736085075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736085075 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 18, 18, 18, 21, 33, 33, 33, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 12, 12, 18, 21, 21, 33, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/227 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1) `ZINC001736085075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736085075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736085075 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 13, 19, 19, 19, 24, 35, 35, 35, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 19, 24, 24, 35, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736085075 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 Building ZINC001736085075 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736085075 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 226) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1) `ZINC001736085075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736085075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736085075 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 18, 18, 18, 21, 33, 33, 33, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 12, 12, 18, 21, 21, 33, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 227) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1) `ZINC001736085075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736085075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736085075 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CNC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 13, 19, 19, 19, 24, 35, 35, 35, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 19, 24, 24, 35, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736085075 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736085075 Building ZINC001736091076 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091076 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/228 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/228' -> `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](NC(=O)C[C@@H]2CCNC2=O)C1) `ZINC001736091076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091076 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 27, 27, 27, 27, 27, 27, 39, 39, 39, 49, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 27, 27, 27, 39, 49, 49, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/229 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/229' -> `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](NC(=O)C[C@@H]2CCNC2=O)C1) `ZINC001736091076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091076 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 29, 29, 29, 29, 29, 29, 40, 40, 40, 49, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091076 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 Building ZINC001736091076 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091076 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 228) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CCNC2=O)C1) `ZINC001736091076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091076 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 27, 27, 27, 27, 27, 27, 39, 39, 39, 49, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 27, 27, 27, 39, 49, 49, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 229) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CCNC2=O)C1) `ZINC001736091076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091076 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 29, 29, 29, 29, 29, 29, 40, 40, 40, 49, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091076 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091076 Building ZINC001736091077 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091077 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/230 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/230' -> `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](NC(=O)C[C@H]2CCNC2=O)C1) `ZINC001736091077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091077 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 31, 40, 40, 40, 45, 50, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 40, 45, 45, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/231 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/231' -> `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](NC(=O)C[C@H]2CCNC2=O)C1) `ZINC001736091077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091077 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 26, 36, 36, 36, 47, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 36, 47, 47, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091077 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 Building ZINC001736091077 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091077 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 230) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CCNC2=O)C1) `ZINC001736091077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091077 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 31, 40, 40, 40, 45, 50, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 40, 45, 45, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 231) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CCNC2=O)C1) `ZINC001736091077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091077 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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', '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, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 26, 36, 36, 36, 47, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 36, 47, 47, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091077 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091077 Building ZINC001736091094 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091094 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/232 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/232' -> `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](NC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736091094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091094 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 28, 28, 28, 28, 28, 28, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 34, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/233 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/233' -> `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](NC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736091094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091094 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 29, 29, 29, 29, 29, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 34, 50, 50, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091094 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 Building ZINC001736091094 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091094 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 232) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736091094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091094 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 28, 28, 28, 28, 28, 28, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 34, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 233) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736091094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091094 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 29, 29, 29, 29, 29, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 34, 50, 50, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091094 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091094 Building ZINC001736091095 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091095 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/234 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/234' -> `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](NC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736091095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091095 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 26, 26, 26, 26, 26, 26, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 34, 50, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/235 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/235' -> `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](NC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736091095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091095 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 28, 28, 28, 28, 28, 28, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 28, 28, 28, 34, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091095 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 Building ZINC001736091095 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091095 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 234) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736091095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091095 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 26, 26, 26, 26, 26, 26, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 34, 50, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 235) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736091095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736091095 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 28, 28, 28, 28, 28, 28, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 28, 28, 28, 34, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091095 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091095 Building ZINC001736091230 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091230 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/236 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736091230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736091230 none Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 47, 47, 42, 42, 42, 42, 42, 16, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 150, 50, 47, 42, 42, 42, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 287 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/237 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736091230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736091230 none Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 46, 46, 34, 34, 34, 34, 34, 14, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 150, 50, 46, 34, 34, 34, 34, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 294 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091230 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 Building ZINC001736091230 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091230 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 236) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736091230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736091230 none Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 47, 47, 42, 42, 42, 42, 42, 16, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 150, 50, 47, 42, 42, 42, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 287 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 237) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736091230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736091230 none Cn1c(O)ncc1C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 46, 46, 34, 34, 34, 34, 34, 14, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 150, 50, 46, 34, 34, 34, 34, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 294 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091230 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091230 Building ZINC001736091285 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091285 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/238 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/238' -> `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](NC(=O)c2cc(C(N)=O)c[nH]2)C1) `ZINC001736091285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091285 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc(C(N)=O)c[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 37, 37, 37, 37, 37, 37, 43, 43, 43, 46, 46, 46, 50, 50, 46, 46, 46, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 37, 37, 43, 46, 50, 50, 46, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/239 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/239' -> `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](NC(=O)c2cc(C(N)=O)c[nH]2)C1) `ZINC001736091285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091285 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc(C(N)=O)c[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 37, 37, 37, 43, 43, 43, 50, 50, 43, 43, 43, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 30, 30, 30, 30, 37, 43, 50, 50, 43, 30, 30] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091285 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 Building ZINC001736091285 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091285 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 238) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc(C(N)=O)c[nH]2)C1) `ZINC001736091285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091285 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc(C(N)=O)c[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 37, 37, 37, 37, 37, 37, 43, 43, 43, 46, 46, 46, 50, 50, 46, 46, 46, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 37, 37, 43, 46, 50, 50, 46, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 239) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc(C(N)=O)c[nH]2)C1) `ZINC001736091285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091285 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc(C(N)=O)c[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 37, 37, 37, 43, 43, 43, 50, 50, 43, 43, 43, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 30, 30, 30, 30, 37, 43, 50, 50, 43, 30, 30] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091285 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091285 Building ZINC001736091430 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091430 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/240 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/240' -> `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](NC(=O)c2cc3n(n2)CCO3)C1) `ZINC001736091430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091430 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc3n(n2)CCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/241 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/241' -> `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](NC(=O)c2cc3n(n2)CCO3)C1) `ZINC001736091430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091430 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc3n(n2)CCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091430 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 Building ZINC001736091430 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091430 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 240) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc3n(n2)CCO3)C1) `ZINC001736091430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091430 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc3n(n2)CCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 241) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc3n(n2)CCO3)C1) `ZINC001736091430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736091430 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)c2cc3n(n2)CCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091430 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091430 Building ZINC001736091645 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091645 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/242 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091645 none CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 22, 35, 15, 15, 11, 11, 11, 11, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 15, 11, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 35] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/243 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091645 none CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 22, 34, 14, 14, 8, 8, 8, 8, 8, 5, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 50, 50, 50, 50, 50, 34, 34, 14, 8, 8, 8, 8, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 34] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091645 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 Building ZINC001736091645 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091645 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 242) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091645 none CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 22, 35, 15, 15, 11, 11, 11, 11, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 15, 11, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 35] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 243) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091645 none CCN1C[C@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 22, 34, 14, 14, 8, 8, 8, 8, 8, 5, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 50, 50, 50, 50, 50, 34, 34, 14, 8, 8, 8, 8, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 34] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091645 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091645 Building ZINC001736091646 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091646 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/244 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091646 none CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 20, 29, 14, 14, 10, 10, 10, 10, 10, 7, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 14, 10, 10, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 29] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/245 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091646 none CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 18, 31, 11, 11, 9, 9, 9, 9, 9, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31, 11, 9, 9, 9, 9, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091646 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 Building ZINC001736091646 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091646 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 244) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091646 none CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 20, 29, 14, 14, 10, 10, 10, 10, 10, 7, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 14, 10, 10, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 29] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 245) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001736091646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736091646 none CCN1C[C@@H](C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 18, 31, 11, 11, 9, 9, 9, 9, 9, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31, 11, 9, 9, 9, 9, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091646 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091646 Building ZINC001736091890 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091890 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/246 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/246' -> `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](NC(=O)C[C@@H]2CC(=O)NC2=O)C1) `ZINC001736091890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091890 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 12, 12, 12, 12, 12, 12, 20, 20, 20, 42, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 20, 42, 42, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/247 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/247' -> `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](NC(=O)C[C@@H]2CC(=O)NC2=O)C1) `ZINC001736091890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091890 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 12, 12, 12, 12, 19, 19, 19, 46, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 12, 12, 12, 12, 19, 46, 46, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091890 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 Building ZINC001736091890 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091890 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 246) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CC(=O)NC2=O)C1) `ZINC001736091890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091890 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 12, 12, 12, 12, 12, 12, 20, 20, 20, 42, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 20, 42, 42, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 247) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CC(=O)NC2=O)C1) `ZINC001736091890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091890 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 12, 12, 12, 12, 19, 19, 19, 46, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 12, 12, 12, 12, 19, 46, 46, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091890 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091890 Building ZINC001736091891 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091891 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/248 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/248' -> `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](NC(=O)C[C@H]2CC(=O)NC2=O)C1) `ZINC001736091891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091891 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 9, 9, 9, 9, 9, 9, 20, 20, 20, 41, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 9, 9, 9, 9, 20, 41, 41, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/249 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/249' -> `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](NC(=O)C[C@H]2CC(=O)NC2=O)C1) `ZINC001736091891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091891 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 14, 14, 14, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 14, 14, 14, 14, 19, 44, 44, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091891 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 Building ZINC001736091891 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736091891 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 248) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CC(=O)NC2=O)C1) `ZINC001736091891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736091891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091891 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 9, 9, 9, 9, 9, 9, 20, 20, 20, 41, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 9, 9, 9, 9, 20, 41, 41, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 249) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CC(=O)NC2=O)C1) `ZINC001736091891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736091891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736091891 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C[C@H]2CC(=O)NC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 14, 14, 14, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 14, 14, 14, 14, 19, 44, 44, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736091891 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736091891 Building ZINC001736095817 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736095817 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/250 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1) `ZINC001736095817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736095817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095817 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 23, 32, 32, 37, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 23, 23, 32, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/251 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1) `ZINC001736095817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736095817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095817 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 19, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 19, 19, 25, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736095817 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 Building ZINC001736095817 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736095817 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 250) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1) `ZINC001736095817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736095817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095817 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 23, 32, 32, 37, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 23, 23, 32, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 251) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1) `ZINC001736095817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736095817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095817 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 19, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 19, 19, 25, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736095817 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095817 Building ZINC001736095818 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736095818 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/252 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1) `ZINC001736095818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736095818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095818 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 11, 23, 31, 31, 37, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/253 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1) `ZINC001736095818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736095818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095818 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 19, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736095818 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 Building ZINC001736095818 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736095818 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 252) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1) `ZINC001736095818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736095818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095818 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 11, 23, 31, 31, 37, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 253) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1) `ZINC001736095818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736095818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736095818 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 19, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736095818 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736095818 Building ZINC001736104517 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736104517 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/254 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1) `ZINC001736104517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736104517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104517 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 12, 12, 12, 12, 12, 12, 28, 39, 39, 42, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 28, 28, 39, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/255 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1) `ZINC001736104517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736104517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104517 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 25, 39, 39, 41, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 25, 25, 39, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736104517 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 Building ZINC001736104517 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736104517 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 254) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1) `ZINC001736104517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736104517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104517 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 12, 12, 12, 12, 12, 12, 28, 39, 39, 42, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 28, 28, 39, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 255) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1) `ZINC001736104517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736104517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104517 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 25, 39, 39, 41, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 25, 25, 39, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736104517 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104517 Building ZINC001736104518 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736104518 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/256 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1) `ZINC001736104518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736104518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104518 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 14, 14, 14, 14, 14, 14, 27, 40, 40, 41, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 27, 27, 40, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/257 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1) `ZINC001736104518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736104518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104518 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 13, 13, 13, 13, 13, 13, 26, 37, 37, 41, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 26, 26, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736104518 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 Building ZINC001736104518 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736104518 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 256) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1) `ZINC001736104518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736104518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104518 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 14, 14, 14, 14, 14, 14, 27, 40, 40, 41, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 27, 27, 40, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 257) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1) `ZINC001736104518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736104518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736104518 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 13, 13, 13, 13, 13, 13, 26, 37, 37, 41, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 26, 26, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736104518 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736104518 Building ZINC001736107983 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736107983 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/258 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1) `ZINC001736107983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736107983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736107983 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 33, 39, 41, 48, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 17, 17, 23, 33, 33, 40, 40, 41, 41, 48, 48, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/259 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1) `ZINC001736107983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736107983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736107983 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 18, 18, 18, 18, 18, 18, 18, 24, 24, 24, 35, 40, 42, 49, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 18, 18, 24, 35, 35, 41, 41, 42, 42, 49, 49, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736107983 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 Building ZINC001736107983 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736107983 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 258) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1) `ZINC001736107983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736107983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736107983 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 33, 39, 41, 48, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 17, 17, 23, 33, 33, 40, 40, 41, 41, 48, 48, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 259) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1) `ZINC001736107983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736107983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736107983 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 18, 18, 18, 18, 18, 18, 18, 24, 24, 24, 35, 40, 42, 49, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 18, 18, 24, 35, 35, 41, 41, 42, 42, 49, 49, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736107983 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736107983 Building ZINC001736109063 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736109063 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/260 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736109063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736109063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 13, 13, 13, 13, 13, 13, 22, 35, 35, 39, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 22, 22, 35, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/261 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736109063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736109063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 11, 11, 11, 11, 11, 11, 22, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736109063 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 Building ZINC001736109063 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736109063 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 260) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736109063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736109063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 13, 13, 13, 13, 13, 13, 22, 35, 35, 39, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 22, 22, 35, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 261) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1) `ZINC001736109063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736109063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 11, 11, 11, 11, 11, 11, 22, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736109063 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109063 Building ZINC001736109064 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736109064 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/262 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736109064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736109064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109064 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 27, 37, 37, 40, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/263 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736109064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736109064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109064 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 24, 36, 36, 40, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 24, 24, 36, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736109064 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 Building ZINC001736109064 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736109064 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 262) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736109064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736109064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109064 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 27, 37, 37, 40, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 263) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1) `ZINC001736109064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736109064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736109064 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@H]2CCC(=O)NC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 24, 36, 36, 40, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 24, 24, 36, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736109064 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736109064 Building ZINC001736111346 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736111346 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/264 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111346 none CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/265 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111346 none CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736111346 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 Building ZINC001736111346 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736111346 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 264) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111346 none CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 265) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111346 none CC[C@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736111346 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111346 Building ZINC001736111348 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736111348 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/266 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111348 none CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 35, 15, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 35, 35, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/267 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111348 none CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 15, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736111348 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 Building ZINC001736111348 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736111348 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 266) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111348 none CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 35, 15, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 35, 35, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 267) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001736111348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736111348 none CC[C@@]1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 15, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736111348 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736111348 Building ZINC001736114841 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736114841 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/268 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001736114841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736114841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736114841 none CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 38, 38, 23, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 38, 23, 23, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/269 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001736114841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736114841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736114841 none CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 42, 40, 40, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 50, 50, 50, 50, 40, 22, 22, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736114841 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 Building ZINC001736114841 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736114841 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 268) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001736114841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736114841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736114841 none CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 38, 38, 23, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 38, 23, 23, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 269) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001736114841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736114841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736114841 none CNC(=O)C1(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 42, 40, 40, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 50, 50, 50, 50, 40, 22, 22, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736114841 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736114841 Building ZINC001736117165 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736117165 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/270 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736117165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736117165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736117165 none CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 50, 44, 44, 32, 15, 15, 15, 15, 15, 6, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 44, 32, 32, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/271 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736117165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736117165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736117165 none CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 50, 40, 40, 28, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 40, 28, 28, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736117165 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 Building ZINC001736117165 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736117165 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 270) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736117165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736117165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736117165 none CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 50, 44, 44, 32, 15, 15, 15, 15, 15, 6, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 44, 32, 32, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 271) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736117165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736117165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736117165 none CN1C(=O)CC[C@H]1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 50, 40, 40, 28, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 40, 28, 28, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736117165 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736117165 Building ZINC001736119303 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736119303 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/272 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1) `ZINC001736119303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736119303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736119303 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 10, 10, 10, 10, 10, 10, 15, 22, 22, 22, 41, 43, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 15, 15, 22, 41, 41, 43, 43, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/273 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1) `ZINC001736119303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736119303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736119303 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 38, 41, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 15, 15, 20, 38, 38, 41, 41, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736119303 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 Building ZINC001736119303 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736119303 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 272) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1) `ZINC001736119303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736119303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736119303 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 10, 10, 10, 10, 10, 10, 15, 22, 22, 22, 41, 43, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 15, 15, 22, 41, 41, 43, 43, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 273) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1) `ZINC001736119303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736119303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736119303 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)CCn2cnnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 38, 41, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 15, 15, 20, 38, 38, 41, 41, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736119303 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736119303 Building ZINC001736120858 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736120858 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/274 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736120858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736120858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736120858 none Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 33, 33, 33, 21, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 33, 21, 21, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/275 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736120858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736120858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736120858 none Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 22, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 34, 22, 22, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736120858 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 Building ZINC001736120858 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736120858 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 274) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736120858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736120858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736120858 none Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 33, 33, 33, 21, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 33, 21, 21, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 275) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736120858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736120858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736120858 none Cc1nonc1CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 22, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 34, 22, 22, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736120858 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736120858 Building ZINC001736128392 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736128392 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/276 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736128392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736128392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736128392 none CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 1, 1, 8, 8, 5, 1, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 10, 6, 10, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 36, 36, 36, 36, 36, 25, 25, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/277 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736128392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736128392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736128392 none CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 1, 1, 8, 8, 5, 1, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 22, 10, 6, 10, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 36, 36, 36, 36, 36, 22, 22, 6, 6, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736128392 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 Building ZINC001736128392 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736128392 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 276) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736128392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736128392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736128392 none CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 1, 1, 8, 8, 5, 1, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 10, 6, 10, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 36, 36, 36, 36, 36, 25, 25, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 277) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736128392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736128392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736128392 none CCOCC(=O)N1C[C@@H](c2cnn(C)c2)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 1, 1, 8, 8, 5, 1, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 22, 10, 6, 10, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 36, 36, 36, 36, 36, 22, 22, 6, 6, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736128392 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736128392 Building ZINC001736132465 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736132465 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/278 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736132465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736132465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736132465 none CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 36, 36, 36, 36, 36, 36, 44, 44, 50, 50, 50, 50, 50, 50, 36, 19, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 36, 36, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/279 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736132465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736132465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736132465 none CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 36, 36, 36, 46, 46, 50, 50, 50, 50, 50, 50, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 36, 36, 50, 50, 50, 50, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736132465 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 Building ZINC001736132465 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736132465 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 278) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736132465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736132465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736132465 none CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 36, 36, 36, 36, 36, 36, 44, 44, 50, 50, 50, 50, 50, 50, 36, 19, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 36, 36, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 279) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736132465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736132465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736132465 none CCO[C@@H]1CN(C(=O)c2cc(C)[nH]n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 36, 36, 36, 46, 46, 50, 50, 50, 50, 50, 50, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 36, 36, 50, 50, 50, 50, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736132465 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736132465 Building ZINC001736136301 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736136301 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/280 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C) `ZINC001736136301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736136301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001736136301 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 18, 18, 18, 40, 35, 50, 50, 50, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 18, 40, 40, 46, 46, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/281 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C) `ZINC001736136301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736136301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001736136301 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 20, 20, 20, 46, 34, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 20, 46, 46, 49, 49, 45, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736136301 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 Building ZINC001736136301 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736136301 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 280) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C) `ZINC001736136301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736136301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001736136301 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 18, 18, 18, 40, 35, 50, 50, 50, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 18, 40, 40, 46, 46, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 281) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C) `ZINC001736136301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736136301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001736136301 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 20, 20, 20, 46, 34, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 20, 46, 46, 49, 49, 45, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736136301 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136301 Building ZINC001736136684 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736136684 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/282 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O) `ZINC001736136684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736136684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736136684 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 27, 27, 27, 43, 46, 45, 49, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 27, 43, 43, 46, 46, 46, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/283 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O) `ZINC001736136684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736136684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736136684 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 27, 27, 27, 37, 44, 44, 50, 50, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 27, 37, 37, 44, 44, 44, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736136684 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 Building ZINC001736136684 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736136684 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 282) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O) `ZINC001736136684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736136684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736136684 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 27, 27, 27, 43, 46, 45, 49, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 27, 43, 43, 46, 46, 46, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 283) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O) `ZINC001736136684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736136684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736136684 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN(C)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 27, 27, 27, 37, 44, 44, 50, 50, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 27, 37, 37, 44, 44, 44, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736136684 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136684 Building ZINC001736136903 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736136903 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/284 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1) `ZINC001736136903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736136903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001736136903 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 28, 28, 28, 49, 50, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 28, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/285 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1) `ZINC001736136903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736136903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001736136903 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 31, 31, 31, 49, 50, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 31, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736136903 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 Building ZINC001736136903 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736136903 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 284) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1) `ZINC001736136903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736136903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001736136903 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 28, 28, 28, 49, 50, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 28, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 285) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1) `ZINC001736136903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736136903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001736136903 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 31, 31, 31, 49, 50, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 31, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736136903 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736136903 Building ZINC001736137008 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736137008 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/286 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC) `ZINC001736137008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736137008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137008 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 7, 19, 19, 19, 30, 31, 31, 31, 50, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 19, 30, 30, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/287 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC) `ZINC001736137008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736137008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137008 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 20, 20, 20, 33, 34, 34, 34, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 20, 33, 33, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736137008 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 Building ZINC001736137008 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736137008 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 286) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC) `ZINC001736137008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736137008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137008 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 7, 19, 19, 19, 30, 31, 31, 31, 50, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 19, 30, 30, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 287) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC) `ZINC001736137008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736137008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137008 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 20, 20, 20, 33, 34, 34, 34, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 20, 33, 33, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736137008 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137008 Building ZINC001736137657 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736137657 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/288 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736137657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736137657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137657 none CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 23, 23, 23, 23, 23, 23, 27, 27, 45, 45, 45, 50, 50, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 23, 23, 45, 45, 45, 50, 50, 50, 50, 50, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/289 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736137657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736137657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137657 none CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 25, 25, 42, 42, 42, 48, 50, 22, 12, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 22, 22, 42, 42, 42, 48, 48, 50, 50, 50, 22, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736137657 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 Building ZINC001736137657 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736137657 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 288) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736137657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736137657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137657 none CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 23, 23, 23, 23, 23, 23, 27, 27, 45, 45, 45, 50, 50, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 23, 23, 45, 45, 45, 50, 50, 50, 50, 50, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 289) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736137657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736137657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137657 none CCO[C@@H]1CN(C(=O)[C@@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 25, 25, 42, 42, 42, 48, 50, 22, 12, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 22, 22, 42, 42, 42, 48, 48, 50, 50, 50, 22, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736137657 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137657 Building ZINC001736137658 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736137658 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/290 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736137658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736137658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137658 none CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 29, 29, 42, 42, 42, 49, 50, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 25, 25, 42, 42, 42, 49, 49, 50, 50, 50, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/291 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736137658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736137658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137658 none CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 24, 24, 24, 24, 24, 24, 26, 26, 39, 39, 39, 49, 50, 24, 16, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 24, 24, 39, 39, 39, 49, 49, 50, 50, 50, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736137658 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 Building ZINC001736137658 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736137658 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 290) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736137658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736137658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137658 none CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 29, 29, 42, 42, 42, 49, 50, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 25, 25, 42, 42, 42, 49, 49, 50, 50, 50, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 291) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736137658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736137658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736137658 none CCO[C@@H]1CN(C(=O)[C@H](C)COC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 24, 24, 24, 24, 24, 24, 26, 26, 39, 39, 39, 49, 50, 24, 16, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 24, 24, 39, 39, 39, 49, 49, 50, 50, 50, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736137658 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736137658 Building ZINC001736138132 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736138132 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/292 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736138132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736138132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736138132 none CCO[C@@H]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 31, 40, 40, 50, 50, 50, 50, 50, 31, 17, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 31, 31, 50, 50, 50, 50, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/293 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736138132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736138132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736138132 none CCO[C@@H]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 32, 32, 32, 32, 32, 32, 40, 40, 50, 50, 50, 50, 50, 32, 15, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 32, 32, 50, 50, 50, 50, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736138132 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 Building ZINC001736138132 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736138132 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 292) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736138132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736138132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736138132 none CCO[C@@H]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 31, 40, 40, 50, 50, 50, 50, 50, 31, 17, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 31, 31, 50, 50, 50, 50, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 293) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736138132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736138132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736138132 none CCO[C@@H]1CN(C(=O)c2cn(C)nn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 32, 32, 32, 32, 32, 32, 40, 40, 50, 50, 50, 50, 50, 32, 15, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 32, 32, 50, 50, 50, 50, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736138132 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736138132 Building ZINC001736142173 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736142173 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/294 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736142173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736142173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736142173 none CCO[C@@H]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 31, 31, 31, 31, 31, 31, 39, 39, 50, 50, 50, 50, 31, 15, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 31, 31, 50, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/295 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736142173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736142173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736142173 none CCO[C@@H]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 38, 33, 33, 33, 33, 33, 33, 42, 42, 49, 49, 49, 49, 33, 14, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 33, 33, 49, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736142173 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 Building ZINC001736142173 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736142173 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 294) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736142173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736142173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736142173 none CCO[C@@H]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 35, 31, 31, 31, 31, 31, 31, 39, 39, 50, 50, 50, 50, 31, 15, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 31, 31, 50, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 295) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736142173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736142173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736142173 none CCO[C@@H]1CN(C(=O)c2csnn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 38, 33, 33, 33, 33, 33, 33, 42, 42, 49, 49, 49, 49, 33, 14, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 33, 33, 49, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736142173 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736142173 Building ZINC001736144797 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736144797 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/296 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736144797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736144797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736144797 none CCO[C@@H]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 19, 19, 19, 19, 19, 19, 25, 25, 49, 50, 50, 50, 50, 50, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/297 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736144797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736144797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736144797 none CCO[C@@H]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 18, 18, 18, 18, 18, 18, 21, 21, 44, 50, 50, 50, 50, 50, 18, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 18, 18, 44, 44, 50, 50, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 189 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736144797 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 Building ZINC001736144797 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736144797 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 296) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736144797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736144797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736144797 none CCO[C@@H]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 19, 19, 19, 19, 19, 19, 25, 25, 49, 50, 50, 50, 50, 50, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 297) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736144797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736144797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736144797 none CCO[C@@H]1CN(C(=O)Cc2cnc[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 18, 18, 18, 18, 18, 18, 21, 21, 44, 50, 50, 50, 50, 50, 18, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 18, 18, 44, 44, 50, 50, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 189 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736144797 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736144797 Building ZINC001736151167 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736151167 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/298 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736151167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736151167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151167 none C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 14, 32, 32, 47, 50, 50, 14, 14, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 3, 5, 1, 1, 1, 1, 1, 1, 32, 32, 32, 47, 47, 50, 50, 14, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/299 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736151167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736151167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151167 none C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 32, 32, 45, 50, 50, 17, 17, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 32, 32, 32, 45, 45, 50, 50, 17, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736151167 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 Building ZINC001736151167 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736151167 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 298) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736151167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736151167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151167 none C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 14, 32, 32, 47, 50, 50, 14, 14, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 3, 5, 1, 1, 1, 1, 1, 1, 32, 32, 32, 47, 47, 50, 50, 14, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 299) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736151167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736151167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151167 none C[C@@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 32, 32, 45, 50, 50, 17, 17, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 32, 32, 32, 45, 45, 50, 50, 17, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736151167 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151167 Building ZINC001736151168 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736151168 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/300 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736151168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736151168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151168 none C[C@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 48, 50, 50, 14, 14, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 3, 5, 1, 1, 1, 2, 2, 2, 29, 29, 29, 48, 48, 50, 50, 14, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 230 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/301 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736151168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736151168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151168 none C[C@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 33, 33, 49, 50, 50, 17, 17, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 33, 33, 33, 49, 49, 50, 50, 17, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736151168 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 Building ZINC001736151168 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736151168 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 300) grep: /scratch/xiaobo/45881/xch-8058115.60/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](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736151168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736151168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151168 none C[C@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 48, 50, 50, 14, 14, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 3, 5, 1, 1, 1, 2, 2, 2, 29, 29, 29, 48, 48, 50, 50, 14, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 230 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 301) grep: /scratch/xiaobo/45881/xch-8058115.60/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](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736151168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736151168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736151168 none C[C@H](CC(N)=O)C(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 33, 33, 49, 50, 50, 17, 17, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 33, 33, 33, 49, 49, 50, 50, 17, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736151168 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151168 Building ZINC001736151250 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736151250 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/302 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736151250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736151250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736151250 none CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 35, 25, 25, 25, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 35, 35, 25, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/303 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736151250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736151250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736151250 none CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 31, 31, 31, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 38, 31, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736151250 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 Building ZINC001736151250 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736151250 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 302) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736151250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736151250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736151250 none CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 35, 25, 25, 25, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 35, 35, 25, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 303) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736151250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736151250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736151250 none CNC(=O)NCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 31, 31, 31, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 38, 31, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736151250 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736151250 Building ZINC001736152308 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736152308 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/304 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1) `ZINC001736152308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736152308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152308 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', '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', '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, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 21, 21, 21, 46, 50, 50, 50, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 21, 50, 50, 50, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 163 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/305 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1) `ZINC001736152308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736152308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152308 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', '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', '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, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 30, 30, 30, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 30, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736152308 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 Building ZINC001736152308 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736152308 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 304) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1) `ZINC001736152308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736152308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152308 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', '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', '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, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 21, 21, 21, 46, 50, 50, 50, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 21, 50, 50, 50, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 163 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 305) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1) `ZINC001736152308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736152308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152308 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)C2(NC(N)=O)CC2)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', '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', '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, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 30, 30, 30, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 30, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736152308 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152308 Building ZINC001736152660 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736152660 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/306 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736152660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736152660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152660 none CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 33, 42, 24, 21, 24, 21, 21, 21, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 42, 33, 33, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 212 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/307 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736152660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736152660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152660 none CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 30, 38, 20, 18, 20, 18, 18, 18, 18, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 30, 30, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 220 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736152660 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 Building ZINC001736152660 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736152660 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 306) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736152660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736152660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152660 none CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 33, 42, 24, 21, 24, 21, 21, 21, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 42, 33, 33, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 212 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 307) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736152660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736152660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736152660 none CCNC(=O)CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 30, 38, 20, 18, 20, 18, 18, 18, 18, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 30, 30, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 220 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736152660 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736152660 Building ZINC001736156930 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736156930 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/308 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736156930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736156930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736156930 none CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 39, 29, 28, 29, 28, 28, 28, 28, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 39, 39, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/309 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736156930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736156930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736156930 none CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 39, 27, 24, 27, 24, 24, 24, 24, 24, 24, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 39, 39, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736156930 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 Building ZINC001736156930 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736156930 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 308) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736156930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736156930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736156930 none CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 39, 29, 28, 29, 28, 28, 28, 28, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 39, 39, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 309) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736156930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736156930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736156930 none CNC(=O)NCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 39, 27, 24, 27, 24, 24, 24, 24, 24, 24, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 39, 39, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736156930 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736156930 Building ZINC001736157858 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736157858 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/310 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736157858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157858 none C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 43, 46, 50, 50, 50, 50, 50, 50, 50, 13, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/311 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736157858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157858 none C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 39, 48, 50, 50, 50, 50, 50, 50, 50, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 142 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736157858 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 Building ZINC001736157858 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736157858 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 310) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736157858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157858 none C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 43, 46, 50, 50, 50, 50, 50, 50, 50, 13, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 311) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736157858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157858 none C[C@@H]1CCN(C(=O)[C@@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 39, 48, 50, 50, 50, 50, 50, 50, 50, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 142 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736157858 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157858 Building ZINC001736157859 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736157859 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/312 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736157859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157859 none C[C@@H]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 48, 50, 50, 50, 50, 50, 50, 50, 23, 38, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 139 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/313 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736157859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157859 none C[C@@H]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 49, 50, 50, 50, 50, 50, 50, 50, 25, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736157859 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 Building ZINC001736157859 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736157859 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 312) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736157859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157859 none C[C@@H]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 48, 50, 50, 50, 50, 50, 50, 50, 23, 38, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 139 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 313) grep: /scratch/xiaobo/45881/xch-8058115.60/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]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736157859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736157859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736157859 none C[C@@H]1CCN(C(=O)[C@H]2CCCNC2=O)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 49, 50, 50, 50, 50, 50, 50, 50, 25, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736157859 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736157859 Building ZINC001736160096 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736160096 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/314 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736160096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736160096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736160096 none C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 47, 50, 50, 50, 50, 50, 50, 17, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 151 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/315 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736160096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736160096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736160096 none C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 43, 47, 50, 50, 50, 50, 50, 50, 18, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 146 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736160096 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 Building ZINC001736160096 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736160096 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 314) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736160096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736160096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736160096 none C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 47, 50, 50, 50, 50, 50, 50, 17, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 151 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 315) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736160096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736160096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736160096 none C[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 43, 47, 50, 50, 50, 50, 50, 50, 18, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 146 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736160096 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736160096 Building ZINC001736187614 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187614 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/316 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736187614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736187614 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 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, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 16, 20, 23, 38, 50, 50, 50, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 22, 22, 23, 23, 38, 38, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/317 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736187614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736187614 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 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, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 20, 26, 28, 43, 50, 50, 50, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 28, 28, 28, 28, 43, 43, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187614 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 Building ZINC001736187614 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187614 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 316) grep: /scratch/xiaobo/45881/xch-8058115.60/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@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736187614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736187614 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 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, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 16, 20, 23, 38, 50, 50, 50, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 22, 22, 23, 23, 38, 38, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 317) grep: /scratch/xiaobo/45881/xch-8058115.60/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@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736187614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736187614 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 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, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 20, 26, 28, 43, 50, 50, 50, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 28, 28, 28, 28, 43, 43, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187614 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187614 Building ZINC001736187725 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187725 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/318 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1) `ZINC001736187725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736187725 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 22, 40, 40, 40, 50, 50, 40, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 40, 40, 40, 50, 50, 50, 40, 40] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/319 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1) `ZINC001736187725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736187725 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 43, 43, 43, 50, 50, 43, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 43, 43, 43, 50, 50, 50, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187725 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 Building ZINC001736187725 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187725 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 318) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1) `ZINC001736187725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736187725 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 22, 40, 40, 40, 50, 50, 40, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 40, 40, 40, 50, 50, 50, 40, 40] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 319) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1) `ZINC001736187725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736187725 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 43, 43, 43, 50, 50, 43, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 43, 43, 43, 50, 50, 50, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187725 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187725 Building ZINC001736187729 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187729 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/320 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001736187729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187729 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 20, 43, 43, 43, 43, 43, 43, 50, 43, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 43, 43, 50, 50, 50, 50, 50, 43, 43] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/321 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001736187729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187729 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 25, 45, 45, 45, 45, 45, 45, 50, 45, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 45, 50, 50, 50, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187729 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 Building ZINC001736187729 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187729 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 320) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001736187729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187729 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 20, 43, 43, 43, 43, 43, 43, 50, 43, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 43, 43, 50, 50, 50, 50, 50, 43, 43] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 321) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001736187729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187729 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 25, 45, 45, 45, 45, 45, 45, 50, 45, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 45, 50, 50, 50, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187729 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187729 Building ZINC001736187730 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187730 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/322 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001736187730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187730 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 14, 19, 31, 31, 31, 31, 31, 31, 50, 31, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/323 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001736187730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187730 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 21, 31, 31, 31, 31, 31, 31, 50, 31, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187730 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 Building ZINC001736187730 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187730 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 322) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001736187730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187730 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 14, 19, 31, 31, 31, 31, 31, 31, 50, 31, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 323) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001736187730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736187730 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 21, 31, 31, 31, 31, 31, 31, 50, 31, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187730 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187730 Building ZINC001736187931 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187931 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/324 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C) `ZINC001736187931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736187931 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 150, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 298 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/325 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C) `ZINC001736187931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736187931 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 34, 34, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 150, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 285 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187931 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 Building ZINC001736187931 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736187931 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 324) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C) `ZINC001736187931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736187931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736187931 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 150, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 298 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 325) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C) `ZINC001736187931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736187931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736187931 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 34, 34, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 150, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 285 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736187931 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736187931 Building ZINC001736188136 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736188136 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/326 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1) `ZINC001736188136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736188136 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 29, 29, 29, 47, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/327 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1) `ZINC001736188136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736188136 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 27, 27, 27, 43, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188136 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 Building ZINC001736188136 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736188136 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 326) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1) `ZINC001736188136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736188136 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 29, 29, 29, 47, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 327) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1) `ZINC001736188136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736188136 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 27, 27, 27, 43, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188136 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188136 Building ZINC001736188142 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188142 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/328 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/329 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/330 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/330' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/331 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/331' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188142 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 Building ZINC001736188142 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188142 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 328) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 329) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 330) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 331) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188142 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 Building ZINC001736188142 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188142 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 328) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 329) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 330) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 331) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188142 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 Building ZINC001736188142 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188142 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 328) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 329) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 330) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 331) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1) `ZINC001736188142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188142 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 36, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188142 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188142 Building ZINC001736188143 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188143 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/332 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/333 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/334 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/334' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/335 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/335' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188143 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 Building ZINC001736188143 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188143 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 332) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 333) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 334) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 335) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188143 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 Building ZINC001736188143 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188143 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 332) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 333) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 334) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 335) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188143 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 Building ZINC001736188143 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736188143 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 332) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 333) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 334) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 335) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1) `ZINC001736188143.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736188143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001736188143 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CN(C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 36, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188143 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188143 Building ZINC001736188656 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736188656 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/336 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001736188656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001736188656 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 23, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/337 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001736188656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001736188656 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188656 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 Building ZINC001736188656 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736188656 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 336) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001736188656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736188656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001736188656 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 23, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 337) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001736188656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736188656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001736188656 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736188656 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736188656 Building ZINC001736194280 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736194280 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/338 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736194280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736194280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194280 none CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 28, 45, 50, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 10, 28, 28, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/339 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736194280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736194280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194280 none CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 25, 44, 50, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 25, 25, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736194280 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 Building ZINC001736194280 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736194280 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 338) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736194280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736194280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194280 none CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 28, 45, 50, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 10, 28, 28, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 339) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736194280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736194280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194280 none CC[C@@H]1[C@@H](NC(=O)CO[C@@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 25, 44, 50, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 25, 25, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736194280 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194280 Building ZINC001736194281 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736194281 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/340 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736194281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736194281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194281 none CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 28, 47, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 12, 28, 28, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/341 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736194281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736194281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194281 none CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 26, 47, 50, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 26, 26, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736194281 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 Building ZINC001736194281 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736194281 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 340) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736194281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736194281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194281 none CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 28, 47, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 12, 28, 28, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 341) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736194281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736194281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736194281 none CC[C@@H]1[C@@H](NC(=O)CO[C@H]2CCOC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 26, 47, 50, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 26, 26, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736194281 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736194281 Building ZINC001736212093 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736212093 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/342 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736212093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736212093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736212093 none CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 40, 46, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 40, 40, 46, 46, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/343 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736212093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736212093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736212093 none CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 10, 10, 10, 37, 44, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 10, 37, 37, 44, 44, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736212093 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 Building ZINC001736212093 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736212093 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 342) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736212093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736212093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736212093 none CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 40, 46, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 40, 40, 46, 46, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 343) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736212093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736212093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736212093 none CC[C@@H]1[C@@H](NC(=O)CCc2cnn(C)n2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 10, 10, 10, 37, 44, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 10, 37, 37, 44, 44, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736212093 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736212093 Building ZINC001736215764 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736215764 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/344 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736215764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215764 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 6, 9, 9, 9, 9, 9, 9, 9, 27, 42, 44, 27, 41, 41, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 42, 42, 44, 44, 132, 41, 41, 41, 41, 41, 41, 9, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 336 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/345 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736215764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215764 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 5, 7, 8, 8, 8, 8, 8, 8, 21, 36, 39, 21, 34, 34, 35, 35, 35, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 36, 36, 39, 39, 117, 35, 35, 35, 35, 35, 35, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 315 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736215764 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 Building ZINC001736215764 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736215764 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 344) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736215764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215764 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 6, 9, 9, 9, 9, 9, 9, 9, 27, 42, 44, 27, 41, 41, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 42, 42, 44, 44, 132, 41, 41, 41, 41, 41, 41, 9, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 336 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 345) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736215764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215764 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 5, 7, 8, 8, 8, 8, 8, 8, 21, 36, 39, 21, 34, 34, 35, 35, 35, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 36, 36, 39, 39, 117, 35, 35, 35, 35, 35, 35, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 315 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736215764 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215764 Building ZINC001736215766 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736215766 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/346 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736215766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 7, 7, 7, 7, 7, 7, 22, 35, 38, 22, 36, 36, 38, 38, 38, 38, 38, 38, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 35, 35, 38, 38, 114, 38, 38, 38, 38, 38, 38, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 302 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/347 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736215766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 5, 5, 8, 8, 8, 8, 8, 8, 21, 39, 43, 21, 35, 35, 35, 35, 35, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 39, 39, 43, 43, 129, 35, 35, 35, 35, 35, 35, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 353 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736215766 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 Building ZINC001736215766 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736215766 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 346) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736215766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 7, 7, 7, 7, 7, 7, 22, 35, 38, 22, 36, 36, 38, 38, 38, 38, 38, 38, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 35, 35, 38, 38, 114, 38, 38, 38, 38, 38, 38, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 302 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 347) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1) `ZINC001736215766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736215766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736215766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N(CCO)C(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 5, 5, 8, 8, 8, 8, 8, 8, 21, 39, 43, 21, 35, 35, 35, 35, 35, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 39, 39, 43, 43, 129, 35, 35, 35, 35, 35, 35, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 353 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736215766 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736215766 Building ZINC001736221701 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736221701 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/348 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[C@H]2C1) `ZINC001736221701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736221701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736221701 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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', '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, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 7, 8, 8, 8, 8, 8, 8, 8, 11, 11, 22, 22, 26, 36, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 26, 26, 36, 36, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 188 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/349 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[C@H]2C1) `ZINC001736221701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736221701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736221701 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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', '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, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 18, 20, 24, 33, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 18, 18, 20, 20, 24, 24, 33, 33, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 189 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736221701 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 Building ZINC001736221701 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736221701 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 348) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[C@H]2C1) `ZINC001736221701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736221701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736221701 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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', '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, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 7, 8, 8, 8, 8, 8, 8, 8, 11, 11, 22, 22, 26, 36, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 26, 26, 36, 36, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 188 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 349) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[C@H]2C1) `ZINC001736221701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736221701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736221701 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CCCCC(N)=O)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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', '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, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 18, 20, 24, 33, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 18, 18, 20, 20, 24, 24, 33, 33, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 189 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736221701 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736221701 Building ZINC001736222051 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736222051 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/350 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[C@H]2C1) `ZINC001736222051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736222051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222051 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 10, 13, 13, 13, 13, 13, 13, 13, 15, 15, 25, 37, 37, 37, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 25, 25, 37, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/351 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[C@H]2C1) `ZINC001736222051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736222051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222051 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 10, 14, 14, 14, 14, 14, 14, 14, 18, 18, 24, 40, 40, 40, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 24, 24, 40, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736222051 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 Building ZINC001736222051 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736222051 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 350) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[C@H]2C1) `ZINC001736222051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736222051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222051 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 10, 13, 13, 13, 13, 13, 13, 13, 15, 15, 25, 37, 37, 37, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 25, 25, 37, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 351) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[C@H]2C1) `ZINC001736222051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736222051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222051 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)CNC(=O)C3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 10, 14, 14, 14, 14, 14, 14, 14, 18, 18, 24, 40, 40, 40, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 24, 24, 40, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736222051 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222051 Building ZINC001736222206 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736222206 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/352 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[C@H]2C1) `ZINC001736222206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736222206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222206 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 13, 13, 21, 21, 21, 39, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 21, 39, 39, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/353 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[C@H]2C1) `ZINC001736222206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736222206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222206 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 10, 12, 12, 12, 12, 12, 12, 12, 14, 14, 24, 24, 24, 39, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 24, 39, 39, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736222206 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 Building ZINC001736222206 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736222206 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 352) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[C@H]2C1) `ZINC001736222206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736222206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222206 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 13, 13, 21, 21, 21, 39, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 21, 39, 39, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 353) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[C@H]2C1) `ZINC001736222206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736222206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736222206 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)C(=O)NCC3CC3)C[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 10, 12, 12, 12, 12, 12, 12, 12, 14, 14, 24, 24, 24, 39, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 24, 39, 39, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736222206 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736222206 Building ZINC001736223633 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736223633 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/354 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736223633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223633 none C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 28, 44, 50, 50, 11, 19, 11, 11, 11, 11, 11, 11, 7, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 28, 28, 28, 44, 44, 50, 50, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/355 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736223633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223633 none C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 30, 30, 47, 50, 50, 12, 24, 12, 12, 12, 12, 12, 12, 10, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 30, 30, 30, 47, 47, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 206 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736223633 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 Building ZINC001736223633 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736223633 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 354) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736223633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223633 none C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 28, 44, 50, 50, 11, 19, 11, 11, 11, 11, 11, 11, 7, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 28, 28, 28, 44, 44, 50, 50, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 355) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736223633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223633 none C[C@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 30, 30, 47, 50, 50, 12, 24, 12, 12, 12, 12, 12, 12, 10, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 30, 30, 30, 47, 47, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 206 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736223633 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223633 Building ZINC001736223634 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736223634 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/356 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736223634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223634 none C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 30, 30, 41, 50, 50, 14, 25, 14, 14, 14, 14, 14, 14, 9, 1, 11, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 30, 30, 30, 41, 41, 50, 50, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/357 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736223634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223634 none C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 32, 32, 47, 50, 50, 12, 21, 12, 12, 12, 12, 12, 12, 10, 1, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 32, 32, 32, 47, 47, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736223634 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 Building ZINC001736223634 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736223634 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 356) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736223634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223634 none C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 30, 30, 41, 50, 50, 14, 25, 14, 14, 14, 14, 14, 14, 9, 1, 11, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 30, 30, 30, 41, 41, 50, 50, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 357) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001736223634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736223634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736223634 none C[C@@H](CC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 32, 32, 47, 50, 50, 12, 21, 12, 12, 12, 12, 12, 12, 10, 1, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 32, 32, 32, 47, 47, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736223634 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736223634 Building ZINC001636722457 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636722457 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/358 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1) `ZINC001636722457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636722457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001636722457 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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, 10, 10, 10, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 16, 16, 8, 16, 16, 4, 4, 4, 4, 10, 10, 4, 3, 8, 16, 16, 8, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/359 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1) `ZINC001636722457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636722457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001636722457 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 11, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 16, 16, 10, 16, 16, 4, 4, 4, 4, 11, 11, 4, 3, 8, 16, 16, 13, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636722457 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 Building ZINC001636722457 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636722457 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 358) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1) `ZINC001636722457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636722457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001636722457 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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, 10, 10, 10, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 16, 16, 8, 16, 16, 4, 4, 4, 4, 10, 10, 4, 3, 8, 16, 16, 8, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 359) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1) `ZINC001636722457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636722457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001636722457 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1c[nH]nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 11, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 16, 16, 10, 16, 16, 4, 4, 4, 4, 11, 11, 4, 3, 8, 16, 16, 13, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001636722457 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001636722457 Building ZINC001736254815 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254815 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/360 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1) `ZINC001736254815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254815 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 17, 24, 32, 50, 50, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 32, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/361 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1) `ZINC001736254815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254815 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 19, 27, 33, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 19, 33, 33, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254815 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 Building ZINC001736254815 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254815 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 360) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1) `ZINC001736254815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254815 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 17, 24, 32, 50, 50, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 32, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 361) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1) `ZINC001736254815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254815 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 19, 27, 33, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 19, 33, 33, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254815 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254815 Building ZINC001736254816 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254816 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/362 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1) `ZINC001736254816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254816 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 15, 28, 36, 50, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/363 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1) `ZINC001736254816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254816 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 18, 27, 35, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 33, 33, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254816 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 Building ZINC001736254816 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254816 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 362) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1) `ZINC001736254816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254816 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 15, 28, 36, 50, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 363) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1) `ZINC001736254816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736254816 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 18, 27, 35, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 33, 33, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254816 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254816 Building ZINC001736254853 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254853 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/364 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O) `ZINC001736254853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736254853 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 21, 21, 39, 40, 50, 50, 50, 50, 50, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 39, 39, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/365 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O) `ZINC001736254853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736254853 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 22, 22, 42, 42, 50, 50, 50, 50, 50, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254853 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 Building ZINC001736254853 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254853 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 364) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O) `ZINC001736254853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736254853 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 21, 21, 39, 40, 50, 50, 50, 50, 50, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 39, 39, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 365) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O) `ZINC001736254853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736254853 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 22, 22, 42, 42, 50, 50, 50, 50, 50, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254853 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254853 Building ZINC001736254905 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254905 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/366 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C) `ZINC001736254905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736254905 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 29, 42, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/367 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C) `ZINC001736254905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736254905 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 31, 45, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254905 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 Building ZINC001736254905 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736254905 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 366) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C) `ZINC001736254905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736254905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736254905 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 29, 42, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 367) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C) `ZINC001736254905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736254905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736254905 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COCc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 31, 45, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736254905 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736254905 Building ZINC001736255164 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255164 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/368 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1) `ZINC001736255164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736255164 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 23, 48, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/369 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1) `ZINC001736255164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736255164 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 24, 49, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255164 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 Building ZINC001736255164 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255164 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 368) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1) `ZINC001736255164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736255164 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 23, 48, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 369) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1) `ZINC001736255164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736255164 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 24, 49, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255164 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255164 Building ZINC001736255502 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255502 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/370 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1) `ZINC001736255502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736255502 none Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 14, 31, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/371 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1) `ZINC001736255502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736255502 none Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 29, 49, 12, 29, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255502 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 Building ZINC001736255502 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255502 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 370) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1) `ZINC001736255502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736255502 none Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 14, 31, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 371) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1) `ZINC001736255502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736255502 none Cc1cc(NC(=O)C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 29, 49, 12, 29, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255502 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255502 Building ZINC001736255732 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255732 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/372 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255732 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 13, 30, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/373 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255732 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 15, 29, 10, 15, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255732 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 Building ZINC001736255732 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255732 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 372) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255732 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 13, 30, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 373) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255732 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 15, 29, 10, 15, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255732 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255732 Building ZINC001736255734 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255734 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/374 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255734 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 13, 37, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/375 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255734 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 14, 32, 11, 14, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 32, 32, 32, 50, 50, 50, 50, 50, 32, 32, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 32, 32] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255734 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 Building ZINC001736255734 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736255734 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 374) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736255734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255734 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 13, 37, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 375) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O) `ZINC001736255734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736255734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736255734 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 14, 32, 11, 14, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 32, 32, 32, 50, 50, 50, 50, 50, 32, 32, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 32, 32] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736255734 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736255734 Building ZINC001736256271 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736256271 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/376 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001736256271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736256271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736256271 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 28, 29, 48, 48, 48, 48, 48, 48, 50, 50, 48, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 48, 48, 48, 48, 50, 50, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/377 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001736256271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736256271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736256271 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 34, 49, 49, 49, 49, 49, 49, 50, 50, 49, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 49, 49, 49, 49, 50, 50, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736256271 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 Building ZINC001736256271 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736256271 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 376) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001736256271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736256271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736256271 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 28, 29, 48, 48, 48, 48, 48, 48, 50, 50, 48, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 48, 48, 48, 48, 50, 50, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 377) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001736256271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736256271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736256271 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 34, 49, 49, 49, 49, 49, 49, 50, 50, 49, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 49, 49, 49, 49, 50, 50, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736256271 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256271 Building ZINC001736256611 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736256611 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/378 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736256611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736256611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736256611 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 16, 21, 24, 39, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 23, 23, 24, 24, 39, 39, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/379 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736256611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736256611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736256611 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 19, 24, 27, 43, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 27, 27, 27, 27, 43, 43, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736256611 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 Building ZINC001736256611 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736256611 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 378) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736256611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736256611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736256611 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 16, 21, 24, 39, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 23, 23, 24, 24, 39, 39, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 379) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O) `ZINC001736256611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736256611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736256611 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 19, 24, 27, 43, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 27, 27, 27, 27, 43, 43, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736256611 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736256611 Building ZINC001451141194 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451141194 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/380 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451141194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451141194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451141194 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 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: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 3, 4, 8, 8, 4, 4, 4, 4, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/381 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451141194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451141194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451141194 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 16, 16, 16, 16, 16, 16, 5, 5, 5, 3, 2, 7, 7, 2, 2, 2, 2, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451141194 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 Building ZINC001451141194 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451141194 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 380) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451141194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451141194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451141194 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 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: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 3, 4, 8, 8, 4, 4, 4, 4, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 381) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451141194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451141194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451141194 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 16, 16, 16, 16, 16, 16, 5, 5, 5, 3, 2, 7, 7, 2, 2, 2, 2, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451141194 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451141194 Building ZINC001736264794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736264794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/382 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736264794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736264794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736264794 none C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 46, 48, 50, 48, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/383 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736264794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736264794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736264794 none C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 47, 49, 50, 49, 50, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736264794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 Building ZINC001736264794 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736264794 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 382) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736264794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736264794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736264794 none C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 46, 48, 50, 48, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 383) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736264794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736264794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736264794 none C[C@@H]1[C@@H](NC(=O)CNC(=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 47, 49, 50, 49, 50, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736264794 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736264794 Building ZINC001451146011 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146011 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/384 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146011 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4] 16 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/385 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146011 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5] 16 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146011 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 Building ZINC001451146011 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146011 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 384) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146011 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4] 16 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 385) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146011 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5] 16 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146011 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146011 Building ZINC001451146096 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146096 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/386 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146096 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4] 20 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/387 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146096 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4] 22 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146096 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 Building ZINC001451146096 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146096 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 386) grep: /scratch/xiaobo/45881/xch-8058115.60/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(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146096 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4] 20 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 387) grep: /scratch/xiaobo/45881/xch-8058115.60/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(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146096 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4] 22 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146096 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146096 Building ZINC001451146129 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146129 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/388 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146129 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4] 24 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/389 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146129 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 15, 20, 20, 20, 20, 20, 20, 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, 20, 5, 5, 5, 5] 22 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146129 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 Building ZINC001451146129 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146129 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 388) grep: /scratch/xiaobo/45881/xch-8058115.60/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(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146129 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4] 24 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 389) grep: /scratch/xiaobo/45881/xch-8058115.60/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(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146129 none O=C(N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 15, 20, 20, 20, 20, 20, 20, 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, 20, 5, 5, 5, 5] 22 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146129 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146129 Building ZINC001451146155 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146155 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/390 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146155 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [12, 3, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5] 17 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/391 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146155 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5] 17 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146155 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 Building ZINC001451146155 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451146155 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 390) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451146155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146155 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [12, 3, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5] 17 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 391) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001451146155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451146155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451146155 none O=C(N1CCS(=O)(=O)[C@H]2COCC[C@@H]21)[C@@]([O-])([SiH3])c1ccc(Cl)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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5] 17 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451146155 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451146155 Building ZINC001736271252 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736271252 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/392 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736271252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736271252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736271252 none C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 10, 10, 10, 38, 45, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 38, 38, 45, 45, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/393 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736271252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736271252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736271252 none C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 11, 11, 11, 39, 45, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 39, 39, 45, 45, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736271252 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 Building ZINC001736271252 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736271252 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 392) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736271252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736271252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736271252 none C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 10, 10, 10, 38, 45, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 38, 38, 45, 45, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 393) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736271252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736271252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736271252 none C[C@@H]1[C@@H](NC(=O)CCn2ccccc2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 11, 11, 11, 39, 45, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 39, 39, 45, 45, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736271252 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736271252 Building ZINC001736277825 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736277825 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/394 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736277825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736277825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277825 none C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 14, 24, 40, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 14, 14, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/395 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736277825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736277825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277825 none C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 17, 34, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 45, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736277825 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 Building ZINC001736277825 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736277825 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 394) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736277825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736277825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277825 none C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 14, 24, 40, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 14, 14, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 395) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736277825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736277825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277825 none C[C@@H]1[C@@H](NC(=O)COC[C@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 17, 34, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 45, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736277825 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277825 Building ZINC001736277826 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736277826 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/396 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736277826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736277826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277826 none C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 13, 24, 41, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 13, 13, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/397 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736277826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736277826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277826 none C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 18, 34, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 43, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736277826 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 Building ZINC001736277826 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736277826 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 396) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736277826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736277826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277826 none C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 13, 24, 41, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 13, 13, 39, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 397) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736277826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736277826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736277826 none C[C@@H]1[C@@H](NC(=O)COC[C@@H]2CCCO2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 18, 34, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 43, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736277826 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736277826 Building ZINC001736278387 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736278387 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/398 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736278387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736278387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736278387 none C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 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: [6, 6, 6, 6, 6, 6, 16, 16, 16, 43, 50, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 43, 43, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/399 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736278387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736278387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736278387 none C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 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: [6, 6, 6, 6, 6, 6, 13, 13, 13, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 42, 42, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736278387 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 Building ZINC001736278387 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736278387 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 398) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736278387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736278387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736278387 none C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 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: [6, 6, 6, 6, 6, 6, 16, 16, 16, 43, 50, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 43, 43, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 399) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736278387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736278387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736278387 none C[C@@H]1[C@@H](NC(=O)CCN2C(=O)CCC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 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: [6, 6, 6, 6, 6, 6, 13, 13, 13, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 42, 42, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736278387 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736278387 Building ZINC001451173689 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173689 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/400 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21) `ZINC001451173689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173689 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 18 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 35 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/401 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21) `ZINC001451173689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173689 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 17 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173689 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 Building ZINC001451173689 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173689 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 400) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21) `ZINC001451173689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173689 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 18 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 35 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 401) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21) `ZINC001451173689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173689 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 17 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173689 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173689 Building ZINC001451173704 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173704 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/402 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21) `ZINC001451173704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173704 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 19 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/403 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21) `ZINC001451173704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173704 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 21 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173704 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 Building ZINC001451173704 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173704 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 402) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21) `ZINC001451173704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173704 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 19 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 403) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21) `ZINC001451173704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173704 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 21 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173704 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173704 Building ZINC001451173706 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173706 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/404 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21) `ZINC001451173706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173706 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 32 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/405 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21) `ZINC001451173706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173706 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173706 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 Building ZINC001451173706 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173706 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 404) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21) `ZINC001451173706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173706 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 32 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 405) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21) `ZINC001451173706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173706 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173706 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173706 Building ZINC001451173708 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173708 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/406 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21) `ZINC001451173708.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173708 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 16 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/407 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21) `ZINC001451173708.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173708 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 14 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 29 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173708 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 Building ZINC001451173708 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451173708 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 406) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21) `ZINC001451173708.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451173708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173708 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 16 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 407) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21) `ZINC001451173708.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451173708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001451173708 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)[C@@H]2COCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 14 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 29 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451173708 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451173708 Building ZINC001736282484 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736282484 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/408 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736282484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736282484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736282484 none C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 22, 17, 37, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 22, 22, 24, 24, 35, 32, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/409 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736282484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736282484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736282484 none C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 26, 20, 37, 50, 50, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 26, 26, 26, 26, 37, 35, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736282484 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 Building ZINC001736282484 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736282484 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 408) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736282484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736282484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736282484 none C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 22, 17, 37, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 22, 22, 24, 24, 35, 32, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 409) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736282484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736282484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736282484 none C[C@@H]1[C@@H](NC(=O)CCCC(=O)N(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 26, 20, 37, 50, 50, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 26, 26, 26, 26, 37, 35, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 55, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736282484 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736282484 Building ZINC001736291713 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736291713 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/410 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/411 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/412 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/412' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/413 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/413' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736291713 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 Building ZINC001736291713 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736291713 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 410) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 411) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 412) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 413) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736291713 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 Building ZINC001736291713 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736291713 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 410) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 411) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 412) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 413) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736291713 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 Building ZINC001736291713 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736291713 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 410) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 411) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 412) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 27, 46, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 413) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736291713.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736291713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736291713 none C[C@@H]1[C@@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [57, 55, 56, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736291713 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736291713 Building ZINC001451233474 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451233474 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/414 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451233474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451233474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451233474 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 2, 7, 7, 2, 2, 2, 2, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/415 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451233474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451233474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451233474 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 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: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 3, 4, 8, 8, 4, 4, 4, 4, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451233474 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 Building ZINC001451233474 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451233474 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 414) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451233474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451233474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451233474 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 2, 7, 7, 2, 2, 2, 2, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 415) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1) `ZINC001451233474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451233474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001451233474 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1cncc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 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: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 3, 4, 8, 8, 4, 4, 4, 4, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451233474 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451233474 Building ZINC001736331068 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736331068 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/416 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1) `ZINC001736331068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736331068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736331068 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 8, 8, 10, 10, 18, 19, 21, 36, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 20, 20, 21, 20, 36, 36, 50, 50, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/417 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1) `ZINC001736331068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736331068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736331068 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 9, 9, 17, 18, 20, 36, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 19, 19, 19, 20, 36, 36, 50, 50, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736331068 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 Building ZINC001736331068 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736331068 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 416) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1) `ZINC001736331068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736331068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736331068 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 8, 8, 10, 10, 18, 19, 21, 36, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 20, 20, 21, 20, 36, 36, 50, 50, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 417) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1) `ZINC001736331068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736331068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736331068 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 9, 9, 17, 18, 20, 36, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 19, 19, 19, 20, 36, 36, 50, 50, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736331068 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736331068 Building ZINC001736332263 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736332263 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/418 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1) `ZINC001736332263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736332263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332263 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 14, 14, 27, 27, 27, 44, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 27, 44, 44, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/419 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1) `ZINC001736332263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736332263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332263 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 14, 14, 26, 26, 26, 47, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 26, 47, 47, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736332263 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 Building ZINC001736332263 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736332263 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 418) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1) `ZINC001736332263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736332263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332263 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 14, 14, 27, 27, 27, 44, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 27, 44, 44, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 419) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1) `ZINC001736332263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736332263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332263 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)C(=O)NCC3CC3)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 14, 14, 26, 26, 26, 47, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 26, 47, 47, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736332263 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332263 Building ZINC001736332550 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736332550 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/420 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736332550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736332550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332550 none COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 42, 24, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 46, 46, 24, 24, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/421 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736332550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736332550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332550 none COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 22, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 46, 46, 22, 22, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736332550 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 Building ZINC001736332550 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736332550 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 420) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736332550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736332550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332550 none COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 42, 24, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 46, 46, 24, 24, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 421) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736332550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736332550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736332550 none COCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 22, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 46, 46, 22, 22, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736332550 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736332550 Building ZINC001451282723 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451282723 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/422 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001451282723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451282723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001451282723 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 6, 19, 21, 23, 23, 23, 23, 28, 28, 35, 35, 35, 35, 23, 23, 5, 5, 5, 5, 5, 5, 4, 21, 21, 63, 23, 23, 23, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/423 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001451282723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451282723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001451282723 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 6, 22, 24, 25, 25, 25, 25, 29, 29, 35, 35, 35, 35, 25, 25, 5, 5, 5, 5, 5, 5, 4, 24, 24, 72, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 25, 25, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451282723 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 Building ZINC001451282723 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451282723 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 422) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001451282723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451282723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001451282723 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 6, 19, 21, 23, 23, 23, 23, 28, 28, 35, 35, 35, 35, 23, 23, 5, 5, 5, 5, 5, 5, 4, 21, 21, 63, 23, 23, 23, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 423) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001451282723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451282723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001451282723 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 6, 22, 24, 25, 25, 25, 25, 29, 29, 35, 35, 35, 35, 25, 25, 5, 5, 5, 5, 5, 5, 4, 24, 24, 72, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 25, 25, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451282723 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451282723 Building ZINC001736345419 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736345419 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/424 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736345419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736345419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736345419 none COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 26, 24, 18, 7, 4, 7, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 39, 39, 26, 26, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/425 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736345419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736345419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736345419 none COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 24, 22, 16, 7, 4, 7, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 39, 39, 24, 24, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736345419 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 Building ZINC001736345419 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736345419 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 424) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736345419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736345419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736345419 none COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 26, 24, 18, 7, 4, 7, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 39, 39, 26, 26, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 425) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001736345419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736345419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736345419 none COCCCOCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 24, 22, 16, 7, 4, 7, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 39, 39, 24, 24, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736345419 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736345419 Building ZINC001736353085 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353085 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/426 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736353085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736353085 none C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 22, 22, 40, 40, 40, 50, 50, 40, 40, 40, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 40, 50, 50, 40, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/427 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736353085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736353085 none C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 44, 44, 44, 50, 50, 44, 44, 44, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 44, 50, 50, 44, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353085 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 Building ZINC001736353085 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353085 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 426) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736353085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736353085 none C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 22, 22, 40, 40, 40, 50, 50, 40, 40, 40, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 40, 50, 50, 40, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 427) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736353085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736353085 none C[C@@H]1CN(C(=O)c2cc(C(N)=O)c[nH]2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 44, 44, 44, 50, 50, 44, 44, 44, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 44, 50, 50, 44, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353085 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353085 Building ZINC001736353445 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353445 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/428 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736353445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353445 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 50, 50, 50, 50, 50, 50, 50, 34, 23, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/429 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736353445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353445 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 48, 50, 50, 50, 50, 50, 50, 50, 50, 41, 24, 41, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353445 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 Building ZINC001736353445 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353445 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 428) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736353445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353445 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 50, 50, 50, 50, 50, 50, 50, 34, 23, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 429) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736353445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353445 none C[C@@H]1CN(C(=O)[C@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 48, 50, 50, 50, 50, 50, 50, 50, 50, 41, 24, 41, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353445 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353445 Building ZINC001736353446 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353446 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/430 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736353446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353446 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 50, 50, 50, 50, 50, 50, 50, 35, 25, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/431 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736353446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353446 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353446 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 Building ZINC001736353446 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353446 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 430) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736353446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353446 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 50, 50, 50, 50, 50, 50, 50, 35, 25, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 431) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736353446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353446 none C[C@@H]1CN(C(=O)[C@@]2(C)CCNC(=O)C2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353446 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353446 Building ZINC001736353465 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353465 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/432 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353465 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 25, 32, 23, 25, 23, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/433 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353465 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 28, 32, 27, 28, 27, 27, 16, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353465 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 Building ZINC001736353465 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353465 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 432) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353465 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 25, 32, 23, 25, 23, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 433) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353465 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 28, 32, 27, 28, 27, 27, 16, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353465 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353465 Building ZINC001736353467 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353467 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/434 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353467 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 25, 31, 24, 25, 24, 24, 15, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/435 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353467 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 30, 33, 29, 30, 29, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353467 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 Building ZINC001736353467 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736353467 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 434) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353467 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 25, 31, 24, 25, 24, 24, 15, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 435) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1) `ZINC001736353467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736353467 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 30, 33, 29, 30, 29, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353467 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353467 Building ZINC001736353943 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353943 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/436 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/437 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/438 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/438' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/439 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/439' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353943 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 Building ZINC001736353943 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353943 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 436) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 437) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 438) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 439) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353943 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 Building ZINC001736353943 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353943 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 436) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 437) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 438) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 439) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353943 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 Building ZINC001736353943 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353943 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 436) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 437) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 34, 37, 34, 34, 20, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 438) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 439) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353943.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353943 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 50, 36, 39, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353943 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353943 Building ZINC001736353944 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353944 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/440 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/441 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/442 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/442' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/443 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/443' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353944 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 Building ZINC001736353944 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353944 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 440) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 441) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 442) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 443) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353944 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 Building ZINC001736353944 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353944 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 440) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 441) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 442) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 443) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353944 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 Building ZINC001736353944 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736353944 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 440) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 441) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 50, 40, 47, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 442) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 443) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001736353944.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736353944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001736353944 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 45, 48, 45, 45, 21, 45, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736353944 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736353944 Building ZINC001736354095 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736354095 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/444 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736354095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736354095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736354095 none C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 30, 30, 47, 50, 50, 50, 50, 50, 50, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 47, 47, 50, 50, 50, 50, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/445 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736354095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736354095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736354095 none C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 44, 50, 50, 50, 50, 50, 50, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 44, 44, 50, 50, 50, 50, 30, 30, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736354095 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 Building ZINC001736354095 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736354095 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 444) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736354095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736354095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736354095 none C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 30, 30, 47, 50, 50, 50, 50, 50, 50, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 47, 47, 50, 50, 50, 50, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 445) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736354095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736354095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736354095 none C[C@@H]1CN(C(=O)Cn2ccccc2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 44, 50, 50, 50, 50, 50, 50, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 44, 44, 50, 50, 50, 50, 30, 30, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736354095 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354095 Building ZINC001736354153 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736354153 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/446 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736354153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736354153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736354153 none C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 21, 21, 34, 34, 50, 50, 50, 50, 50, 20, 13, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 34, 34, 34, 34, 50, 50, 50, 50, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/447 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736354153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736354153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736354153 none C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 50, 50, 50, 50, 50, 21, 14, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 35, 35, 35, 35, 50, 50, 50, 50, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736354153 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 Building ZINC001736354153 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736354153 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 446) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736354153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736354153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736354153 none C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 21, 21, 34, 34, 50, 50, 50, 50, 50, 20, 13, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 34, 34, 34, 34, 50, 50, 50, 50, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 447) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736354153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736354153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736354153 none C[C@@H]1CN(C(=O)CCc2cnn(C)n2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 50, 50, 50, 50, 50, 21, 14, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 35, 35, 35, 35, 50, 50, 50, 50, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736354153 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736354153 Building ZINC001736357455 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736357455 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/448 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1) `ZINC001736357455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736357455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736357455 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 21, 21, 21, 48, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 21, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/449 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1) `ZINC001736357455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736357455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736357455 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 20, 20, 20, 47, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 20, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736357455 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 Building ZINC001736357455 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736357455 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 448) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1) `ZINC001736357455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736357455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736357455 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 21, 21, 21, 48, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 21, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 449) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1) `ZINC001736357455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736357455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736357455 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 20, 20, 20, 47, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 20, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736357455 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736357455 Building ZINC001736364650 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736364650 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/450 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1) `ZINC001736364650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736364650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364650 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 6, 37, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/451 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1) `ZINC001736364650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736364650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364650 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 10, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 32, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736364650 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 Building ZINC001736364650 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736364650 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 450) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1) `ZINC001736364650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736364650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364650 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 6, 37, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 451) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1) `ZINC001736364650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736364650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364650 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 10, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 32, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736364650 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364650 Building ZINC001736364651 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736364651 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/452 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1) `ZINC001736364651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736364651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364651 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 6, 38, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 28, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/453 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1) `ZINC001736364651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736364651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364651 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 10, 10, 10, 40, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 10, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736364651 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 Building ZINC001736364651 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736364651 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 452) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1) `ZINC001736364651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736364651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364651 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 6, 38, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 28, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 453) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1) `ZINC001736364651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736364651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736364651 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 10, 10, 10, 40, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 10, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736364651 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736364651 Building ZINC001736369988 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736369988 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/454 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1) `ZINC001736369988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736369988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369988 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/455 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1) `ZINC001736369988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736369988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369988 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736369988 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 Building ZINC001736369988 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736369988 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 454) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1) `ZINC001736369988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736369988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369988 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 455) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1) `ZINC001736369988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736369988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369988 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736369988 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369988 Building ZINC001736369990 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736369990 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/456 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1) `ZINC001736369990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736369990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369990 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 13, 32, 32, 38, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/457 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1) `ZINC001736369990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736369990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369990 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 34, 34, 41, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736369990 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 Building ZINC001736369990 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736369990 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 456) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1) `ZINC001736369990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736369990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369990 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 13, 32, 32, 38, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 457) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1) `ZINC001736369990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736369990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736369990 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(C)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 34, 34, 41, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736369990 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736369990 Building ZINC001736372361 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736372361 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/458 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O) `ZINC001736372361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736372361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736372361 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 12, 12, 12, 28, 30, 39, 48, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 12, 28, 28, 39, 39, 39, 39, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/459 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O) `ZINC001736372361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736372361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736372361 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 13, 13, 13, 29, 29, 39, 45, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 13, 29, 29, 38, 38, 38, 39, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736372361 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 Building ZINC001736372361 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736372361 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 458) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O) `ZINC001736372361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736372361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736372361 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 12, 12, 12, 28, 30, 39, 48, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 12, 28, 28, 39, 39, 39, 39, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 459) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O) `ZINC001736372361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736372361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001736372361 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 13, 13, 13, 29, 29, 39, 45, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 13, 29, 29, 38, 38, 38, 39, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736372361 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736372361 Building ZINC001736397511 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736397511 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/460 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736397511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736397511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736397511 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 35, 38, 50, 50, 50, 50, 50, 50, 31, 19, 31, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/461 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736397511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736397511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736397511 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 34, 36, 50, 50, 50, 50, 50, 50, 31, 22, 31, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736397511 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 Building ZINC001736397511 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736397511 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 460) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736397511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736397511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736397511 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 35, 38, 50, 50, 50, 50, 50, 50, 31, 19, 31, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 461) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736397511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736397511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736397511 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 34, 36, 50, 50, 50, 50, 50, 50, 31, 22, 31, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736397511 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736397511 Building ZINC001736398453 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736398453 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/462 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736398453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736398453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736398453 none C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 13, 13, 38, 40, 50, 50, 50, 50, 50, 12, 9, 12, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 38, 38, 40, 40, 50, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/463 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736398453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736398453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736398453 none C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 15, 15, 34, 40, 50, 50, 50, 50, 50, 13, 10, 13, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 34, 34, 40, 40, 50, 13, 13, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736398453 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 Building ZINC001736398453 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736398453 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 462) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736398453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736398453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736398453 none C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 13, 13, 38, 40, 50, 50, 50, 50, 50, 12, 9, 12, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 38, 38, 40, 40, 50, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 463) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736398453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736398453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736398453 none C[C@@H]1CN(C(=O)CCc2cnn[nH]2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 15, 15, 34, 40, 50, 50, 50, 50, 50, 13, 10, 13, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 34, 34, 40, 40, 50, 13, 13, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736398453 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398453 Building ZINC001736398571 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736398571 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/464 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=O)N1) `ZINC001736398571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736398571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736398571 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 23, 42, 42, 48, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 23, 23, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/465 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=O)N1) `ZINC001736398571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736398571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736398571 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 24, 42, 42, 47, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 24, 24, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736398571 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 Building ZINC001736398571 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736398571 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 464) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=O)N1) `ZINC001736398571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736398571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736398571 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 23, 42, 42, 48, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 23, 23, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 465) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=O)N1) `ZINC001736398571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736398571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736398571 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 24, 42, 42, 47, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 24, 24, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736398571 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398571 Building ZINC001736398886 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736398886 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/466 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N) `ZINC001736398886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736398886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736398886 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 25, 49, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 25, 25, 49, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/467 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N) `ZINC001736398886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736398886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736398886 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 24, 24, 49, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736398886 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 Building ZINC001736398886 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736398886 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 466) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N) `ZINC001736398886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736398886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736398886 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 25, 49, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 25, 25, 49, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 467) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N) `ZINC001736398886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736398886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736398886 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 24, 24, 49, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736398886 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736398886 Building ZINC001736399264 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736399264 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/468 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736399264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736399264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736399264 none C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 14, 14, 33, 40, 50, 50, 50, 50, 11, 7, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 33, 33, 40, 40, 50, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/469 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736399264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736399264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736399264 none C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 16, 16, 30, 37, 50, 50, 50, 50, 14, 12, 14, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 30, 30, 37, 37, 50, 14, 14, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736399264 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 Building ZINC001736399264 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736399264 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 468) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736399264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736399264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736399264 none C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 14, 14, 33, 40, 50, 50, 50, 50, 11, 7, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 33, 33, 40, 40, 50, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 469) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736399264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736399264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736399264 none C[C@@H]1CN(C(=O)CCn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 16, 16, 30, 37, 50, 50, 50, 50, 14, 12, 14, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 30, 30, 37, 37, 50, 14, 14, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736399264 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399264 Building ZINC001736399348 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736399348 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/470 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736399348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399348 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 50, 50, 33, 41, 33, 33, 33, 33, 33, 24, 33, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/471 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736399348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399348 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 50, 50, 35, 40, 35, 35, 35, 35, 35, 23, 35, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736399348 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 Building ZINC001736399348 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736399348 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 470) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736399348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399348 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 50, 50, 33, 41, 33, 33, 33, 33, 33, 24, 33, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 471) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736399348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399348 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 50, 50, 35, 40, 35, 35, 35, 35, 35, 23, 35, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736399348 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399348 Building ZINC001736399351 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736399351 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/472 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736399351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399351 none CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 50, 28, 36, 28, 28, 28, 28, 28, 21, 28, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/473 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736399351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399351 none CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 50, 50, 30, 35, 30, 30, 30, 30, 30, 19, 30, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736399351 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 Building ZINC001736399351 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736399351 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 472) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736399351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399351 none CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 50, 28, 36, 28, 28, 28, 28, 28, 21, 28, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 473) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736399351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736399351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736399351 none CC(=O)N[C@H](C)C(=O)N1C[C@@H](C)[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 50, 50, 30, 35, 30, 30, 30, 30, 30, 19, 30, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736399351 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736399351 Building ZINC001451382730 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451382730 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/474 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(N2CCCS2(=O)=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001451382730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451382730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001451382730 none O=C(N1CCC(N2CCCS2(=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', 'C.3', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 19, 19, 19, 21, 50, 50, 50, 48, 50, 50, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/475 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(N2CCCS2(=O)=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001451382730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451382730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001451382730 none O=C(N1CCC(N2CCCS2(=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', 'C.3', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 19, 19, 19, 19, 50, 50, 50, 47, 50, 50, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451382730 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 Building ZINC001451382730 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451382730 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 474) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(N2CCCS2(=O)=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001451382730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451382730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001451382730 none O=C(N1CCC(N2CCCS2(=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', 'C.3', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 19, 19, 19, 21, 50, 50, 50, 48, 50, 50, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 475) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(N2CCCS2(=O)=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001451382730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451382730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001451382730 none O=C(N1CCC(N2CCCS2(=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', 'C.3', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 19, 19, 19, 19, 50, 50, 50, 47, 50, 50, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001451382730 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001451382730 Building ZINC001736417353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736417353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/476 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=O)N1) `ZINC001736417353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736417353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736417353 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 24, 48, 48, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 24, 24, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/477 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=O)N1) `ZINC001736417353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736417353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736417353 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 25, 47, 47, 48, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 25, 25, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736417353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 Building ZINC001736417353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736417353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 476) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=O)N1) `ZINC001736417353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736417353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736417353 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 24, 48, 48, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 24, 24, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 477) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=O)N1) `ZINC001736417353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736417353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736417353 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)[C@@H]1CCC(=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 25, 47, 47, 48, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 25, 25, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736417353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736417353 Building ZINC001736431811 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736431811 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/478 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001736431811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736431811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736431811 none CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.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.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 50, 27, 27, 27, 15, 8, 8, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 27, 15, 15, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/479 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001736431811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736431811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736431811 none CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.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.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 50, 26, 26, 26, 12, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 26, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736431811 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 Building ZINC001736431811 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736431811 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 478) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001736431811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736431811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736431811 none CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.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.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 50, 27, 27, 27, 15, 8, 8, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 27, 15, 15, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 479) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001736431811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736431811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736431811 none CC(=O)NCC(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.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.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 50, 26, 26, 26, 12, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 26, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736431811 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736431811 Building ZINC001736433146 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736433146 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/480 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001736433146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736433146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736433146 none COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 28, 19, 19, 19, 19, 19, 19, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 50, 50, 50, 37, 28, 28, 19, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/481 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001736433146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736433146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736433146 none COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 33, 22, 22, 22, 22, 22, 22, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 38, 33, 33, 22, 22, 22, 22, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736433146 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 Building ZINC001736433146 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736433146 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 480) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001736433146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736433146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736433146 none COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 28, 19, 19, 19, 19, 19, 19, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 50, 50, 50, 37, 28, 28, 19, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 481) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001736433146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736433146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736433146 none COC(=O)NCC(=O)N1CC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 33, 22, 22, 22, 22, 22, 22, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 38, 33, 33, 22, 22, 22, 22, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736433146 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433146 Building ZINC001736433527 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736433527 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/482 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/482' -> `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@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2) `ZINC001736433527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736433527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433527 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 37, 37, 37, 37, 37, 37, 37, 37, 42, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/483 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/483' -> `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@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2) `ZINC001736433527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736433527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433527 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 38, 38, 38, 38, 38, 38, 38, 38, 43, 50, 50, 50, 50, 50, 50, 38, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736433527 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 Building ZINC001736433527 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736433527 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 482) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2) `ZINC001736433527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736433527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433527 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 37, 37, 37, 37, 37, 37, 37, 37, 42, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 483) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2) `ZINC001736433527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736433527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433527 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 38, 38, 38, 38, 38, 38, 38, 38, 43, 50, 50, 50, 50, 50, 50, 38, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736433527 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433527 Building ZINC001736433528 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736433528 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/484 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/484' -> `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@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2) `ZINC001736433528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736433528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433528 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 34, 34, 34, 34, 34, 34, 34, 34, 44, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/485 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/485' -> `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@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2) `ZINC001736433528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736433528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433528 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 33, 33, 33, 33, 33, 33, 33, 34, 45, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736433528 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 Building ZINC001736433528 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736433528 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 484) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2) `ZINC001736433528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736433528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433528 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 34, 34, 34, 34, 34, 34, 34, 34, 44, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 485) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2) `ZINC001736433528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736433528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001736433528 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1N(C(=O)[C@H]1COCCO1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 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, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 33, 33, 33, 33, 33, 33, 33, 34, 45, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736433528 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736433528 Building ZINC001736465319 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465319 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/486 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465319 none COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 36, 29, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 44, 44, 36, 36, 16, 16, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/487 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465319 none COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 42, 36, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 42, 42, 20, 20, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465319 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 Building ZINC001736465319 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465319 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 486) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465319 none COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 36, 29, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 44, 44, 36, 36, 16, 16, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 487) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465319 none COCCCOCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 42, 36, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 42, 42, 20, 20, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465319 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465319 Building ZINC001736465355 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465355 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/488 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O) `ZINC001736465355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736465355 none Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 7, 25, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/489 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O) `ZINC001736465355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736465355 none Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 9, 32, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465355 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 Building ZINC001736465355 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465355 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 488) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O) `ZINC001736465355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736465355 none Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 7, 25, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 489) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O) `ZINC001736465355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736465355 none Cn1cc(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 9, 32, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465355 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465355 Building ZINC001736465368 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465368 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/490 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1) `ZINC001736465368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736465368 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 14, 14, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/491 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1) `ZINC001736465368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736465368 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 17, 17, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465368 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 Building ZINC001736465368 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465368 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 490) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1) `ZINC001736465368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736465368 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 14, 14, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 491) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1) `ZINC001736465368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001736465368 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 17, 17, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465368 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465368 Building ZINC001736465387 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465387 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/492 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465387 none COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 24, 11, 24, 24, 8, 11, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 30, 24, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 225 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/493 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465387 none COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 18, 8, 18, 18, 6, 8, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 29, 18, 18, 18, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 224 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465387 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 Building ZINC001736465387 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465387 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 492) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465387 none COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 24, 11, 24, 24, 8, 11, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 30, 24, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 225 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 493) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465387 none COCC(=O)N[C@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 18, 8, 18, 18, 6, 8, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 29, 18, 18, 18, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 224 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465387 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465387 Building ZINC001736465389 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465389 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/494 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465389 none COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 24, 12, 24, 24, 7, 12, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 28, 24, 24, 24, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/495 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465389 none COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 24, 10, 24, 24, 8, 10, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 28, 24, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465389 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 Building ZINC001736465389 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736465389 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 494) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736465389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465389 none COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 24, 12, 24, 24, 7, 12, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 28, 24, 24, 24, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 495) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736465389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736465389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736465389 none COCC(=O)N[C@@H](C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 24, 10, 24, 24, 8, 10, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 28, 24, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736465389 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736465389 Building ZINC001736466062 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466062 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/496 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1) `ZINC001736466062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466062 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/497 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1) `ZINC001736466062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466062 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466062 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 Building ZINC001736466062 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466062 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 496) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1) `ZINC001736466062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466062 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 497) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1) `ZINC001736466062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466062 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466062 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466062 Building ZINC001736466063 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466063 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/498 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1) `ZINC001736466063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/499 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1) `ZINC001736466063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466063 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 Building ZINC001736466063 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466063 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 498) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1) `ZINC001736466063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 499) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1) `ZINC001736466063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466063 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466063 Building ZINC001736466080 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466080 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/500 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466080 none Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 14, 33, 14, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 2, 2, 2, 14, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/501 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466080 none Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 2, 2, 2, 14, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466080 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 Building ZINC001736466080 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466080 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 500) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466080 none Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 14, 33, 14, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 2, 2, 2, 14, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 501) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466080 none Cn1c(=O)cccc1C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 2, 2, 2, 14, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466080 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466080 Building ZINC001736466184 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466184 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/502 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466184 none CC[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 26, 16, 26, 16, 16, 16, 16, 16, 16, 16, 5, 16, 5, 1, 5, 1, 1, 1, 2, 2, 2, 16, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 16, 16, 16, 16, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 49, 49, 49, 49, 49] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/503 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466184 none CC[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 16, 25, 16, 16, 16, 16, 16, 16, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466184 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 Building ZINC001736466184 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466184 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 502) grep: /scratch/xiaobo/45881/xch-8058115.60/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[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466184 none CC[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 26, 16, 26, 16, 16, 16, 16, 16, 16, 16, 5, 16, 5, 1, 5, 1, 1, 1, 2, 2, 2, 16, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 16, 16, 16, 16, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 49, 49, 49, 49, 49] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 503) grep: /scratch/xiaobo/45881/xch-8058115.60/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[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466184 none CC[C@@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 16, 25, 16, 16, 16, 16, 16, 16, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466184 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466184 Building ZINC001736466186 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466186 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/504 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466186 none CC[C@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 15, 29, 15, 15, 15, 15, 15, 15, 15, 4, 15, 4, 1, 4, 1, 1, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/505 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466186 none CC[C@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 12, 24, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466186 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 Building ZINC001736466186 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466186 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 504) grep: /scratch/xiaobo/45881/xch-8058115.60/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@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466186 none CC[C@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 15, 29, 15, 15, 15, 15, 15, 15, 15, 4, 15, 4, 1, 4, 1, 1, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 505) grep: /scratch/xiaobo/45881/xch-8058115.60/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@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O) `ZINC001736466186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736466186 none CC[C@]1(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 12, 24, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466186 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466186 Building ZINC001736466547 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466547 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/506 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466547 none CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 31, 40, 25, 8, 6, 8, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 40, 31, 31, 25, 25, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/507 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466547 none CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 27, 36, 21, 8, 6, 8, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 36, 27, 27, 21, 21, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466547 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 Building ZINC001736466547 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466547 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 506) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466547 none CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 31, 40, 25, 8, 6, 8, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 40, 31, 31, 25, 25, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 507) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736466547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466547 none CCNC(=O)CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 27, 36, 21, 8, 6, 8, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 36, 27, 27, 21, 21, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466547 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466547 Building ZINC001736466558 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466558 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/508 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466558 none C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 26, 38, 11, 26, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 38, 50, 50, 50, 38, 38, 38, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/509 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466558 none C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 32, 8, 22, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 32, 32, 32, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466558 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 Building ZINC001736466558 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466558 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 508) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466558 none C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 26, 38, 11, 26, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 38, 50, 50, 50, 38, 38, 38, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 509) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466558 none C[C@@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 32, 8, 22, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 32, 32, 32, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466558 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466558 Building ZINC001736466561 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466561 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/510 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466561 none C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 26, 36, 10, 26, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 36, 50, 50, 50, 36, 36, 36, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/511 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466561 none C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 32, 8, 21, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 32, 32, 32, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466561 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 Building ZINC001736466561 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466561 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 510) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466561 none C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 26, 36, 10, 26, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 36, 50, 50, 50, 36, 36, 36, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 511) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O) `ZINC001736466561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736466561 none C[C@H](C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 32, 8, 21, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 32, 32, 32, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466561 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466561 Building ZINC001736466683 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466683 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/512 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/513 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/514 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/514' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/515 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/515' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466683 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 Building ZINC001736466683 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466683 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 512) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 513) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 514) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 515) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466683 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 Building ZINC001736466683 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466683 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 512) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 513) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 514) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 515) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466683 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 Building ZINC001736466683 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466683 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 512) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 513) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 514) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 515) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466683 none CN1CCO[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 9, 28, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466683 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466683 Building ZINC001736466685 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466685 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/516 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/517 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/518 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/518' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/519 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/519' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466685 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 Building ZINC001736466685 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466685 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 516) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 517) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 518) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 519) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466685 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 Building ZINC001736466685 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466685 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 516) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 517) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 518) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 519) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466685 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 Building ZINC001736466685 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736466685 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 516) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 517) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 518) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 8, 24, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 519) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1) `ZINC001736466685.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736466685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736466685 none CN1CCO[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466685 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466685 Building ZINC001736466758 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466758 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/520 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1) `ZINC001736466758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466758 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/521 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1) `ZINC001736466758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466758 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 27, 27, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466758 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 Building ZINC001736466758 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736466758 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 520) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1) `ZINC001736466758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736466758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466758 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 521) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1) `ZINC001736466758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736466758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736466758 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CC1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 27, 27, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736466758 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736466758 Building ZINC001736538079 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538079 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/522 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1) `ZINC001736538079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538079 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 35, 35, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/523 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1) `ZINC001736538079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538079 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 32, 32, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538079 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 Building ZINC001736538079 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538079 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 522) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1) `ZINC001736538079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538079 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 35, 35, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 523) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1) `ZINC001736538079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538079 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 32, 32, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538079 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538079 Building ZINC001736538080 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538080 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/524 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1) `ZINC001736538080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538080 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/525 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1) `ZINC001736538080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538080 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538080 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 Building ZINC001736538080 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538080 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 524) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1) `ZINC001736538080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538080 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 31, 31, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 525) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1) `ZINC001736538080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736538080 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538080 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538080 Building ZINC001736538201 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538201 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/526 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001736538201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736538201 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 32, 32, 44, 44, 44, 50, 50, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 20, 20, 20, 20, 44, 50, 50, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/527 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001736538201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736538201 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 38, 38, 38, 50, 50, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 15, 15, 38, 50, 50, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538201 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 Building ZINC001736538201 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538201 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 526) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001736538201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736538201 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 32, 32, 44, 44, 44, 50, 50, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 20, 20, 20, 20, 44, 50, 50, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 527) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001736538201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001736538201 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cc(C(N)=O)c[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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 38, 38, 38, 50, 50, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 15, 15, 38, 50, 50, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538201 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538201 Building ZINC001736538415 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538415 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/528 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538415 none Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 38, 30, 16, 30, 16, 16, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 38, 38, 38, 38, 50, 50, 38, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/529 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538415 none Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 50, 50, 41, 27, 11, 27, 11, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 11, 41, 41, 41, 41, 50, 50, 41, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538415 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 Building ZINC001736538415 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538415 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 528) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538415 none Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 38, 30, 16, 30, 16, 16, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 38, 38, 38, 38, 50, 50, 38, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 529) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538415 none Cn1cc(C(N)=O)cc1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 50, 50, 41, 27, 11, 27, 11, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 11, 41, 41, 41, 41, 50, 50, 41, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538415 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538415 Building ZINC001736538658 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538658 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/530 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736538658 none CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 30, 25, 10, 9, 10, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 38, 40, 34, 34, 25, 25, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/531 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736538658 none CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 25, 21, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 37, 37, 28, 28, 21, 21, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538658 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 Building ZINC001736538658 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538658 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 530) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736538658 none CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 30, 25, 10, 9, 10, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 38, 40, 34, 34, 25, 25, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 531) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736538658 none CNC(=O)CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 25, 21, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 37, 37, 28, 28, 21, 21, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538658 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538658 Building ZINC001736538955 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538955 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/532 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538955 none C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/533 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538955 none C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 27, 50, 9, 27, 9, 9, 9, 9, 9, 9, 9, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538955 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 Building ZINC001736538955 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736538955 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 532) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736538955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538955 none C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 9, 29, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 533) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736538955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736538955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001736538955 none C[C@@H]1OCCO[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 27, 50, 9, 27, 9, 9, 9, 9, 9, 9, 9, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736538955 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736538955 Building ZINC001736539029 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539029 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/534 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/535 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/536 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/536' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/537 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/537' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539029 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 Building ZINC001736539029 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539029 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 534) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 535) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 536) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 537) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539029 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 Building ZINC001736539029 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539029 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 534) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 535) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 536) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 537) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539029 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 Building ZINC001736539029 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539029 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 534) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 535) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 9, 30, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 536) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 537) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539029.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539029 none CCN1CCOC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 9, 31, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539029 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539029 Building ZINC001736539030 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539030 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/538 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/539 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/540 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/540' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/541 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/541' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539030 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 Building ZINC001736539030 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539030 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 538) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 539) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 540) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 541) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539030 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 Building ZINC001736539030 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539030 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 538) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 539) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 540) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 541) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539030 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 Building ZINC001736539030 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001736539030 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 538) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 539) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 540) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 541) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001736539030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001736539030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001736539030 none CCN1CCOC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 10, 32, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 153 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539030 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539030 Building ZINC001736539280 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736539280 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/542 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O) `ZINC001736539280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736539280 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/543 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O) `ZINC001736539280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736539280 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 182 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539280 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 Building ZINC001736539280 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736539280 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 542) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O) `ZINC001736539280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736539280 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 543) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O) `ZINC001736539280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001736539280 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 182 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539280 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539280 Building ZINC001736539287 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736539287 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/544 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539287 none CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 50, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/545 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539287 none CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 8, 20, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539287 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 Building ZINC001736539287 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736539287 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 544) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539287 none CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 50, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 545) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539287 none CN1CC[C@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 8, 20, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539287 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539287 Building ZINC001736539288 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736539288 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/546 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539288 none CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/547 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539288 none CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 50, 8, 25, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539288 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 Building ZINC001736539288 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736539288 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 546) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736539288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539288 none CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 547) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O) `ZINC001736539288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736539288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736539288 none CN1CC[C@@H](C(=O)N2[C@@H]3CC[C@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 50, 8, 25, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736539288 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736539288 Building ZINC001736588620 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736588620 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/548 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736588620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736588620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736588620 none COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 32, 16, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 33, 33, 16, 16, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/549 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736588620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736588620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736588620 none COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 30, 24, 12, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 38, 30, 30, 12, 12, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736588620 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 Building ZINC001736588620 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736588620 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 548) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001736588620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736588620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736588620 none COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 32, 16, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 33, 33, 16, 16, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 549) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001736588620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736588620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736588620 none COCCCOCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 30, 24, 12, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 38, 30, 30, 12, 12, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736588620 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736588620 Building ZINC001736600847 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600847 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/550 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2) `ZINC001736600847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 26, 38, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/551 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2) `ZINC001736600847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 26, 36, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600847 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 Building ZINC001736600847 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600847 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 550) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2) `ZINC001736600847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 26, 38, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 551) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2) `ZINC001736600847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 26, 36, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600847 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600847 Building ZINC001736600850 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600850 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/552 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2) `ZINC001736600850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600850 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 21, 32, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/553 `/scratch/xiaobo/45881/xch-8058115.60/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)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2) `ZINC001736600850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600850 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 21, 31, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600850 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 Building ZINC001736600850 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600850 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 552) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2) `ZINC001736600850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600850 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 21, 32, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 553) grep: /scratch/xiaobo/45881/xch-8058115.60/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)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2) `ZINC001736600850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736600850 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CCNC(=O)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 21, 31, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600850 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600850 Building ZINC001736600936 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600936 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/554 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600936 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 49, 49, 12, 30, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 49, 49, 49, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/555 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600936 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 49, 49, 12, 30, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 49, 49, 49, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600936 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 Building ZINC001736600936 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600936 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 554) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600936 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 49, 49, 12, 30, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 49, 49, 49, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 555) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600936 none CC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 49, 49, 12, 30, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 49, 49, 49, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600936 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600936 Building ZINC001736600938 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600938 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/556 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600938 none CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 50, 14, 34, 14, 14, 14, 14, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/557 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600938 none CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 50, 14, 34, 14, 14, 14, 14, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600938 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 Building ZINC001736600938 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736600938 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 556) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736600938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600938 none CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 50, 14, 34, 14, 14, 14, 14, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 557) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736600938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736600938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736600938 none CC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 50, 14, 34, 14, 14, 14, 14, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736600938 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736600938 Building ZINC001736601051 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736601051 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/558 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736601051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736601051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736601051 none Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 13, 30, 13, 13, 13, 13, 13, 13, 13, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 150, 50, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/559 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736601051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736601051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736601051 none Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 14, 32, 14, 14, 14, 14, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 150, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736601051 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 Building ZINC001736601051 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736601051 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 558) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736601051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736601051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736601051 none Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 13, 30, 13, 13, 13, 13, 13, 13, 13, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 150, 50, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 559) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001736601051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736601051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001736601051 none Cn1c(O)ncc1C(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 14, 32, 14, 14, 14, 14, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 150, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736601051 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601051 Building ZINC001736601317 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736601317 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/560 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736601317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601317 none CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 12, 32, 12, 12, 12, 12, 12, 12, 12, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/561 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736601317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601317 none CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 12, 34, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736601317 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 Building ZINC001736601317 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736601317 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 560) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736601317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601317 none CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 12, 32, 12, 12, 12, 12, 12, 12, 12, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 561) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736601317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601317 none CN1CC[C@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 12, 34, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736601317 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601317 Building ZINC001736601318 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736601318 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/562 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736601318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601318 none CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 12, 33, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/563 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736601318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601318 none CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 12, 32, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736601318 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 Building ZINC001736601318 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736601318 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 562) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736601318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601318 none CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 12, 33, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 563) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001736601318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736601318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001736601318 none CN1CC[C@@H](C(=O)N2C[C@@H]3CCC[C@]3(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 12, 32, 12, 12, 12, 12, 12, 12, 12, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736601318 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736601318 Building ZINC001637091764 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637091764 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/564 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1) `ZINC001637091764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637091764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091764 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 17, 17, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/565 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1) `ZINC001637091764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637091764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091764 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 11, 24, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 16, 16, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637091764 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 Building ZINC001637091764 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637091764 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 564) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1) `ZINC001637091764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637091764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091764 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 17, 17, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 565) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1) `ZINC001637091764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637091764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091764 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 11, 24, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 16, 16, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637091764 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091764 Building ZINC001637091765 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637091765 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/566 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001637091765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637091765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091765 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 22, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 15, 15, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/567 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001637091765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637091765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091765 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 17, 17, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637091765 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 Building ZINC001637091765 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637091765 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 566) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001637091765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637091765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091765 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 22, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 15, 15, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 567) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001637091765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637091765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001637091765 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 17, 17, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637091765 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637091765 Building ZINC001736628954 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736628954 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/568 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/568' -> `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@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2) `ZINC001736628954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736628954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628954 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 31, 31, 31, 31, 31, 31, 31, 31, 37, 37, 50, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/569 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/569' -> `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@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2) `ZINC001736628954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736628954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628954 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 28, 28, 28, 37, 37, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736628954 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 Building ZINC001736628954 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736628954 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 568) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2) `ZINC001736628954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736628954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628954 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 31, 31, 31, 31, 31, 31, 31, 31, 37, 37, 50, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 569) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2) `ZINC001736628954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736628954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628954 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 28, 28, 28, 37, 37, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736628954 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628954 Building ZINC001736628955 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736628955 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/570 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/570' -> `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@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2) `ZINC001736628955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736628955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628955 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 28, 28, 28, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/571 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/571' -> `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@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2) `ZINC001736628955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736628955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628955 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 28, 28, 28, 40, 40, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736628955 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 Building ZINC001736628955 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001736628955 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 570) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2) `ZINC001736628955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001736628955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628955 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 28, 28, 28, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 571) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2) `ZINC001736628955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001736628955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001736628955 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]12CCC[C@H]1CN(C(=O)[C@@H]1CNC(=O)N1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 28, 28, 28, 40, 40, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001736628955 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001736628955 Building ZINC001637151745 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637151745 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/572 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC001637151745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637151745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001637151745 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 19, 19, 6, 19, 19, 6, 4, 4, 4, 4, 14, 14, 4, 6, 6, 6, 19, 19, 7, 19, 19, 6, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/573 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC001637151745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637151745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001637151745 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 3, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 3, 3, 3, 3, 12, 12, 3, 6, 6, 6, 17, 17, 9, 17, 17, 6, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637151745 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 Building ZINC001637151745 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637151745 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 572) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC001637151745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637151745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001637151745 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 19, 19, 6, 19, 19, 6, 4, 4, 4, 4, 14, 14, 4, 6, 6, 6, 19, 19, 7, 19, 19, 6, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 573) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC001637151745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637151745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001637151745 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 3, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 3, 3, 3, 3, 12, 12, 3, 6, 6, 6, 17, 17, 9, 17, 17, 6, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637151745 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637151745 Building ZINC001452387619 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452387619 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/574 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1) `ZINC001452387619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452387619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001452387619 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 23, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 23, 23, 6, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/575 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1) `ZINC001452387619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452387619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001452387619 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 7, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 102 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452387619 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 Building ZINC001452387619 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452387619 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 574) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1) `ZINC001452387619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452387619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001452387619 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 23, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 23, 23, 6, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 575) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1) `ZINC001452387619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452387619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001452387619 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(F)c(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 7, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 102 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452387619 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452387619 Building ZINC001637366607 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637366607 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/576 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F) `ZINC001637366607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637366607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001637366607 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens 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, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 4, 11, 22, 11] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 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/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/577 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F) `ZINC001637366607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637366607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001637366607 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens 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, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 4, 10, 20, 10] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637366607 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 Building ZINC001637366607 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637366607 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 576) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F) `ZINC001637366607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637366607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001637366607 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens 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, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 4, 11, 22, 11] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 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/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 577) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F) `ZINC001637366607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637366607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001637366607 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(O)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens 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, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 4, 10, 20, 10] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637366607 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637366607 Building ZINC001637443622 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637443622 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/578 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1) `ZINC001637443622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637443622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637443622 none CC(C)OC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 2, 2, 5, 5, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/579 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1) `ZINC001637443622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637443622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637443622 none CC(C)OC1(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 6, 6, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637443622 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 Building ZINC001637443622 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637443622 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 578) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1) `ZINC001637443622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637443622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637443622 none CC(C)OC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 2, 2, 5, 5, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 579) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1) `ZINC001637443622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637443622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637443622 none CC(C)OC1(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 6, 6, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637443622 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637443622 Building ZINC001452597514 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597514 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/580 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/581 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/582 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/582' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/583 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/583' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597514 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 Building ZINC001452597514 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597514 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 580) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 581) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 582) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 583) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597514 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 Building ZINC001452597514 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597514 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 580) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 581) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 582) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 583) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597514 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 Building ZINC001452597514 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597514 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 580) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 581) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 582) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 583) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1) `ZINC001452597514.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597514 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 4, 4, 4, 4, 12, 12, 4, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597514 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597514 Building ZINC001452597517 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597517 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/584 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/585 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/586 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/586' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/587 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/587' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597517 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 Building ZINC001452597517 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597517 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 584) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 585) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 586) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 587) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597517 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 Building ZINC001452597517 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597517 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 584) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 585) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 586) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 587) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597517 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 Building ZINC001452597517 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001452597517 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 584) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 585) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 7, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 586) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 587) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1) `ZINC001452597517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001452597517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001452597517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001452597517 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001452597517 Building ZINC001637456985 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637456985 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/588 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [22, 22, 8, 22, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 18, 8, 22, 22, 22, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 18, 18, 54, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/589 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 9, 23, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 18, 9, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 18, 18, 54, 9, 9] 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, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/590 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/590' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 8, 23, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 23, 23, 23, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/591 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/591' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [24, 24, 8, 24, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 24, 24, 24, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637456985 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 Building ZINC001637456985 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637456985 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 588) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [22, 22, 8, 22, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 18, 8, 22, 22, 22, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 18, 18, 54, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 589) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 9, 23, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 18, 9, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 18, 18, 54, 9, 9] 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, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 590) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 8, 23, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 23, 23, 23, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 591) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [24, 24, 8, 24, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 24, 24, 24, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637456985 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 Building ZINC001637456985 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637456985 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 588) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [22, 22, 8, 22, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 18, 8, 22, 22, 22, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 18, 18, 54, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 589) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 9, 23, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 18, 9, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 18, 18, 54, 9, 9] 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, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 590) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 8, 23, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 23, 23, 23, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 591) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [24, 24, 8, 24, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 24, 24, 24, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637456985 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 Building ZINC001637456985 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637456985 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 588) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [22, 22, 8, 22, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 18, 8, 22, 22, 22, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 18, 18, 54, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 589) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 9, 23, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 18, 9, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 18, 18, 54, 9, 9] 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, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 590) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1) `ZINC001637456985.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 23, 8, 23, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 23, 23, 23, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 591) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1) `ZINC001637456985.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637456985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001637456985 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C[C@H](CO)C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [24, 24, 8, 24, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 20, 8, 24, 24, 24, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 20, 20, 60, 8, 8] 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, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637456985 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637456985 Building ZINC001637579917 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637579917 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/592 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1) `ZINC001637579917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637579917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001637579917 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 36, 36, 36, 36, 44, 44, 44, 44, 44, 44, 36, 36, 4, 4, 4, 4, 4, 4, 2, 13, 13, 36, 36, 44, 36, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/593 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1) `ZINC001637579917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637579917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001637579917 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 36, 36, 36, 36, 44, 44, 44, 44, 44, 44, 35, 36, 4, 4, 4, 4, 4, 4, 2, 13, 13, 36, 36, 44, 36, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637579917 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 Building ZINC001637579917 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637579917 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 592) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1) `ZINC001637579917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637579917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001637579917 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 36, 36, 36, 36, 44, 44, 44, 44, 44, 44, 36, 36, 4, 4, 4, 4, 4, 4, 2, 13, 13, 36, 36, 44, 36, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 593) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1) `ZINC001637579917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637579917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001637579917 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(NC(=O)C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 36, 36, 36, 36, 44, 44, 44, 44, 44, 44, 35, 36, 4, 4, 4, 4, 4, 4, 2, 13, 13, 36, 36, 44, 36, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637579917 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637579917 Building ZINC001737187660 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737187660 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/594 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001737187660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737187660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737187660 none CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/595 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001737187660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737187660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737187660 none CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 21, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737187660 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 Building ZINC001737187660 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737187660 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 594) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001737187660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737187660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737187660 none CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 595) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001737187660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737187660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737187660 none CN(CCCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 21, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737187660 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737187660 Building ZINC001637735777 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637735777 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/596 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637735777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735777 none COC(=O)[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 9, 22, 5, 9, 9, 15, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 7, 8, 8, 4, 4, 22, 22, 22, 9, 9, 9, 15, 15, 45, 5, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 165 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/597 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637735777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735777 none COC(=O)[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 5, 18, 2, 5, 5, 13, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 18, 18, 18, 5, 5, 5, 13, 13, 39, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 143 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637735777 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 Building ZINC001637735777 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637735777 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 596) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637735777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735777 none COC(=O)[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 9, 22, 5, 9, 9, 15, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 7, 8, 8, 4, 4, 22, 22, 22, 9, 9, 9, 15, 15, 45, 5, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 165 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 597) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637735777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735777 none COC(=O)[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 5, 18, 2, 5, 5, 13, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 18, 18, 18, 5, 5, 5, 13, 13, 39, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 143 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637735777 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735777 Building ZINC001637735778 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637735778 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/598 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637735778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735778 none COC(=O)[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 6, 17, 2, 6, 6, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 17, 17, 17, 6, 6, 6, 15, 15, 45, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 158 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/599 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637735778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735778 none COC(=O)[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 5, 18, 2, 5, 5, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 18, 18, 18, 5, 5, 5, 12, 12, 36, 2, 4, 4, 4, 8, 8, 7, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 156 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637735778 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 Building ZINC001637735778 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637735778 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 598) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637735778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735778 none COC(=O)[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 6, 17, 2, 6, 6, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 17, 17, 17, 6, 6, 6, 15, 15, 45, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 158 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 599) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001637735778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637735778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001637735778 none COC(=O)[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 5, 18, 2, 5, 5, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 18, 18, 18, 5, 5, 5, 12, 12, 36, 2, 4, 4, 4, 8, 8, 7, 8, 8, 4, 4, 4] 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, 45, 46]) total number of confs: 156 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637735778 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637735778 Building ZINC001637774186 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637774186 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/600 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)c2)cn1) `ZINC001637774186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637774186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774186 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 21, 40, 40, 42, 42, 42, 42, 42, 42, 42, 10, 5, 5, 5, 5, 5, 5, 2, 10, 10, 10, 42, 42, 42, 42, 42, 42, 126, 42, 42, 10, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/601 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)c2)cn1) `ZINC001637774186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637774186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774186 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 21, 36, 36, 38, 38, 38, 38, 38, 38, 38, 10, 5, 5, 5, 5, 5, 5, 2, 10, 10, 10, 38, 38, 38, 38, 38, 38, 114, 38, 38, 10, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637774186 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 Building ZINC001637774186 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637774186 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 600) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)c2)cn1) `ZINC001637774186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637774186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774186 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 21, 40, 40, 42, 42, 42, 42, 42, 42, 42, 10, 5, 5, 5, 5, 5, 5, 2, 10, 10, 10, 42, 42, 42, 42, 42, 42, 126, 42, 42, 10, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 601) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)c2)cn1) `ZINC001637774186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637774186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774186 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 21, 36, 36, 38, 38, 38, 38, 38, 38, 38, 10, 5, 5, 5, 5, 5, 5, 2, 10, 10, 10, 38, 38, 38, 38, 38, 38, 114, 38, 38, 10, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637774186 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774186 Building ZINC001637774188 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637774188 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/602 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)c2)cn1) `ZINC001637774188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637774188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774188 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 9, 9, 9, 9, 18, 38, 38, 40, 40, 40, 40, 40, 40, 40, 9, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 40, 40, 40, 40, 40, 40, 120, 40, 40, 9, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/603 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)c2)cn1) `ZINC001637774188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637774188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774188 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 18, 39, 39, 41, 41, 41, 41, 41, 41, 41, 10, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 41, 41, 41, 41, 41, 41, 123, 41, 41, 10, 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, 43, 44, 45]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637774188 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 Building ZINC001637774188 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637774188 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 602) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)c2)cn1) `ZINC001637774188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637774188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774188 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 9, 9, 9, 9, 18, 38, 38, 40, 40, 40, 40, 40, 40, 40, 9, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 40, 40, 40, 40, 40, 40, 120, 40, 40, 9, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 603) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)c2)cn1) `ZINC001637774188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637774188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001637774188 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)N3CCC[C@@H](O)C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 18, 39, 39, 41, 41, 41, 41, 41, 41, 41, 10, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 41, 41, 41, 41, 41, 41, 123, 41, 41, 10, 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, 43, 44, 45]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001637774188 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001637774188 Building ZINC001737447018 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737447018 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/604 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001737447018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737447018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737447018 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 17, 17, 17, 41, 42, 49, 49, 49, 49, 49, 49, 50, 50, 49, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 17, 41, 41, 41, 41, 49, 49, 49, 49, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/605 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001737447018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737447018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737447018 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 6, 18, 18, 18, 46, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 18, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737447018 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 Building ZINC001737447018 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737447018 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 604) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001737447018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737447018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737447018 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 17, 17, 17, 41, 42, 49, 49, 49, 49, 49, 49, 50, 50, 49, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 17, 41, 41, 41, 41, 49, 49, 49, 49, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 605) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001737447018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737447018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001737447018 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 6, 18, 18, 18, 46, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 18, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737447018 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737447018 Building ZINC001638076912 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638076912 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/606 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O) `ZINC001638076912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638076912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001638076912 none Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 11, 22] 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/607 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O) `ZINC001638076912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638076912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001638076912 none Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 11, 22] 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638076912 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 Building ZINC001638076912 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638076912 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 606) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O) `ZINC001638076912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638076912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001638076912 none Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 11, 22] 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 607) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O) `ZINC001638076912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638076912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001638076912 none Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 11, 22] 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638076912 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638076912 Building ZINC001737855151 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737855151 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/608 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001737855151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737855151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001737855151 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 22, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 33, 36, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 30, 30, 30, 30, 30, 30, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/609 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001737855151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737855151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001737855151 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 36, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 31, 31, 31, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 223 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737855151 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 Building ZINC001737855151 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737855151 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 608) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001737855151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737855151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001737855151 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 22, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 33, 36, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 30, 30, 30, 30, 30, 30, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 609) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001737855151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737855151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001737855151 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 36, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 31, 31, 31, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 223 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737855151 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737855151 Building ZINC001737892458 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737892458 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/610 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1) `ZINC001737892458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737892458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001737892458 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1 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', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 7, 19, 26, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 220 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/611 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1) `ZINC001737892458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737892458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001737892458 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1 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', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 7, 19, 25, 40, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 7, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 25, 25, 40, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737892458 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 Building ZINC001737892458 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001737892458 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 610) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1) `ZINC001737892458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001737892458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001737892458 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1 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', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 7, 19, 26, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 220 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 611) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1) `ZINC001737892458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001737892458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001737892458 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)C1CC1 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', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 7, 19, 25, 40, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 7, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 25, 25, 40, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001737892458 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001737892458 Building ZINC001638149911 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638149911 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/612 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/612' -> `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)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 36, 36, 29, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 36, 36, 36, 36, 36, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/613 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/613' -> `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)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 14, 14, 14, 14, 14, 26, 35, 35, 26, 35, 35, 14, 14, 5, 5, 5, 5, 5, 5, 2, 10, 10, 42, 14, 14, 14, 14, 26, 26, 35, 35, 26, 35, 35, 14, 14, 14, 14, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/614 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/614' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 35, 35, 29, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 35, 35, 35, 35, 35, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/615 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/615' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 16, 21, 21, 21, 21, 21, 32, 42, 42, 39, 42, 42, 21, 21, 4, 4, 4, 4, 4, 4, 2, 11, 11, 63, 21, 21, 21, 21, 32, 32, 42, 42, 38, 42, 42, 21, 21, 21, 21, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638149911 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 Building ZINC001638149911 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638149911 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 612) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 36, 36, 29, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 36, 36, 36, 36, 36, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 613) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 14, 14, 14, 14, 14, 26, 35, 35, 26, 35, 35, 14, 14, 5, 5, 5, 5, 5, 5, 2, 10, 10, 42, 14, 14, 14, 14, 26, 26, 35, 35, 26, 35, 35, 14, 14, 14, 14, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 614) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 35, 35, 29, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 35, 35, 35, 35, 35, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 615) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 16, 21, 21, 21, 21, 21, 32, 42, 42, 39, 42, 42, 21, 21, 4, 4, 4, 4, 4, 4, 2, 11, 11, 63, 21, 21, 21, 21, 32, 32, 42, 42, 38, 42, 42, 21, 21, 21, 21, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638149911 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 Building ZINC001638149911 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638149911 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 612) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 36, 36, 29, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 36, 36, 36, 36, 36, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 613) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 14, 14, 14, 14, 14, 26, 35, 35, 26, 35, 35, 14, 14, 5, 5, 5, 5, 5, 5, 2, 10, 10, 42, 14, 14, 14, 14, 26, 26, 35, 35, 26, 35, 35, 14, 14, 14, 14, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 614) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 35, 35, 29, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 35, 35, 35, 35, 35, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 615) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 16, 21, 21, 21, 21, 21, 32, 42, 42, 39, 42, 42, 21, 21, 4, 4, 4, 4, 4, 4, 2, 11, 11, 63, 21, 21, 21, 21, 32, 32, 42, 42, 38, 42, 42, 21, 21, 21, 21, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638149911 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 Building ZINC001638149911 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638149911 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 612) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 36, 36, 29, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 36, 36, 36, 36, 36, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 613) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 14, 14, 14, 14, 14, 26, 35, 35, 26, 35, 35, 14, 14, 5, 5, 5, 5, 5, 5, 2, 10, 10, 42, 14, 14, 14, 14, 26, 26, 35, 35, 26, 35, 35, 14, 14, 14, 14, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 614) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 25, 35, 35, 29, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 2, 10, 10, 45, 15, 15, 15, 15, 25, 25, 35, 35, 35, 35, 35, 15, 15, 15, 15, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 615) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)CC2)cn1) `ZINC001638149911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638149911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001638149911 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CC[N@](Cc3ccccc3)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 16, 21, 21, 21, 21, 21, 32, 42, 42, 39, 42, 42, 21, 21, 4, 4, 4, 4, 4, 4, 2, 11, 11, 63, 21, 21, 21, 21, 32, 32, 42, 42, 38, 42, 42, 21, 21, 21, 21, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638149911 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638149911 Building ZINC001638192779 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192779 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/616 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1) `ZINC001638192779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192779 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 2, 6, 9, 19, 19, 19, 19, 19, 19, 19, 19, 31, 19, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 19, 19, 19, 19, 57, 31, 31, 93, 19, 19] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 271 number of broken/clashed sets: 151 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/617 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1) `ZINC001638192779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192779 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 2, 6, 11, 20, 20, 20, 20, 20, 20, 20, 20, 35, 20, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 20, 20, 20, 20, 60, 35, 35, 105, 20, 20] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 302 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192779 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 Building ZINC001638192779 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192779 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 616) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1) `ZINC001638192779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192779 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 2, 6, 9, 19, 19, 19, 19, 19, 19, 19, 19, 31, 19, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 19, 19, 19, 19, 57, 31, 31, 93, 19, 19] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 271 number of broken/clashed sets: 151 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 617) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1) `ZINC001638192779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192779 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 2, 6, 11, 20, 20, 20, 20, 20, 20, 20, 20, 35, 20, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 20, 20, 20, 20, 60, 35, 35, 105, 20, 20] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 302 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192779 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192779 Building ZINC001638192780 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192780 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/618 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1) `ZINC001638192780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192780 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 8, 12, 18, 18, 18, 18, 18, 18, 18, 18, 37, 18, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 4, 18, 18, 18, 18, 54, 37, 37, 111, 18, 18] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/619 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1) `ZINC001638192780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192780 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 7, 10, 16, 16, 16, 16, 16, 16, 16, 16, 30, 16, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 16, 16, 16, 16, 48, 30, 30, 90, 16, 16] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 270 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192780 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 Building ZINC001638192780 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192780 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 618) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1) `ZINC001638192780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192780 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 8, 12, 18, 18, 18, 18, 18, 18, 18, 18, 37, 18, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 4, 18, 18, 18, 18, 54, 37, 37, 111, 18, 18] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 619) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1) `ZINC001638192780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192780 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 7, 10, 16, 16, 16, 16, 16, 16, 16, 16, 30, 16, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 16, 16, 16, 16, 48, 30, 30, 90, 16, 16] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 270 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192780 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192780 Building ZINC001638192781 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192781 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/620 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1) `ZINC001638192781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192781 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 1, 1, 1, 2, 8, 10, 19, 19, 19, 19, 19, 19, 19, 19, 37, 19, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 19, 19, 19, 19, 57, 37, 37, 111, 19, 19] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 322 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/621 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1) `ZINC001638192781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192781 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 2, 7, 9, 17, 17, 17, 17, 17, 17, 17, 17, 29, 17, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 17, 17, 17, 17, 51, 29, 29, 87, 17, 17] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192781 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 Building ZINC001638192781 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192781 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 620) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1) `ZINC001638192781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192781 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 1, 1, 1, 2, 8, 10, 19, 19, 19, 19, 19, 19, 19, 19, 37, 19, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 19, 19, 19, 19, 57, 37, 37, 111, 19, 19] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 322 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 621) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1) `ZINC001638192781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192781 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 2, 7, 9, 17, 17, 17, 17, 17, 17, 17, 17, 29, 17, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 17, 17, 17, 17, 51, 29, 29, 87, 17, 17] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192781 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192781 Building ZINC001638192782 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192782 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/622 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1) `ZINC001638192782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192782 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 2, 8, 9, 18, 18, 18, 18, 18, 18, 18, 18, 34, 18, 3, 3, 3, 10, 10, 10, 10, 10, 3, 3, 3, 18, 18, 18, 18, 54, 34, 34, 102, 18, 18] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 301 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/623 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1) `ZINC001638192782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192782 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 1, 1, 1, 2, 8, 9, 18, 18, 18, 18, 18, 18, 18, 18, 37, 18, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 18, 18, 18, 18, 54, 37, 37, 111, 18, 18] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 325 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192782 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 Building ZINC001638192782 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638192782 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 622) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1) `ZINC001638192782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638192782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192782 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 2, 8, 9, 18, 18, 18, 18, 18, 18, 18, 18, 34, 18, 3, 3, 3, 10, 10, 10, 10, 10, 3, 3, 3, 18, 18, 18, 18, 54, 34, 34, 102, 18, 18] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 301 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 623) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1) `ZINC001638192782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638192782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638192782 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 1, 1, 1, 2, 8, 9, 18, 18, 18, 18, 18, 18, 18, 18, 37, 18, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 18, 18, 18, 18, 54, 37, 37, 111, 18, 18] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 325 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638192782 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638192782 Building ZINC001638193719 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638193719 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/624 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC001638193719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638193719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001638193719 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 37, 37, 7, 25, 7, 7, 7, 3, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 50, 50, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 37, 37, 37, 37] 50 rigid atoms, others: [39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/625 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC001638193719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638193719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001638193719 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 34, 34, 34, 34, 6, 25, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 50, 50, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 34, 34, 34, 34] 50 rigid atoms, others: [39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638193719 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 Building ZINC001638193719 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638193719 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 624) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC001638193719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638193719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001638193719 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 37, 37, 7, 25, 7, 7, 7, 3, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 50, 50, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 37, 37, 37, 37] 50 rigid atoms, others: [39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 625) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC001638193719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638193719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001638193719 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 34, 34, 34, 34, 6, 25, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 50, 50, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 34, 34, 34, 34] 50 rigid atoms, others: [39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638193719 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638193719 Building ZINC001453807751 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453807751 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/626 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C) `ZINC001453807751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453807751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807751 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 9, 9, 23, 9, 24, 24, 24, 24, 24, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 23, 23, 69, 24, 24, 24, 24] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/627 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C) `ZINC001453807751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453807751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807751 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 21, 11, 27, 27, 27, 27, 27, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 6, 21, 21, 63, 27, 27, 27, 27] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001453807751 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 Building ZINC001453807751 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453807751 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 626) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C) `ZINC001453807751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453807751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807751 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 9, 9, 23, 9, 24, 24, 24, 24, 24, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 23, 23, 69, 24, 24, 24, 24] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 627) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C) `ZINC001453807751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453807751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807751 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 21, 11, 27, 27, 27, 27, 27, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 6, 21, 21, 63, 27, 27, 27, 27] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001453807751 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807751 Building ZINC001453807754 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453807754 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/628 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C) `ZINC001453807754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453807754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807754 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 21, 10, 27, 27, 27, 27, 27, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 21, 21, 63, 27, 27, 27, 27] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/629 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C) `ZINC001453807754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453807754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807754 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 24, 10, 26, 26, 26, 26, 26, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 6, 24, 24, 72, 26, 26, 26, 26] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 218 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001453807754 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 Building ZINC001453807754 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453807754 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 628) grep: /scratch/xiaobo/45881/xch-8058115.60/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C) `ZINC001453807754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453807754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807754 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 21, 10, 27, 27, 27, 27, 27, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 21, 21, 63, 27, 27, 27, 27] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 629) grep: /scratch/xiaobo/45881/xch-8058115.60/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C) `ZINC001453807754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453807754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001453807754 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1nncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 24, 10, 26, 26, 26, 26, 26, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 6, 24, 24, 72, 26, 26, 26, 26] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 218 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001453807754 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001453807754 Building ZINC001638328706 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638328706 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/630 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2) `ZINC001638328706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638328706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638328706 none Cc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/631 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2) `ZINC001638328706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638328706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638328706 none Cc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638328706 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 Building ZINC001638328706 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638328706 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 630) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2) `ZINC001638328706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638328706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638328706 none Cc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 631) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2) `ZINC001638328706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638328706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638328706 none Cc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 4, 5, 19, 19, 5, 5, 5, 5, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638328706 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638328706 Building ZINC001738187591 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738187591 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/632 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738187591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187591 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 2, 5, 15, 15, 23, 47, 48, 48, 48, 48, 48, 50, 50, 48, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 15, 48, 48, 48, 48, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/633 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738187591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187591 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 9, 17, 17, 22, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 9, 9, 17, 49, 49, 49, 49, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 168 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738187591 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 Building ZINC001738187591 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738187591 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 632) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738187591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187591 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 2, 5, 15, 15, 23, 47, 48, 48, 48, 48, 48, 50, 50, 48, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 15, 48, 48, 48, 48, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 633) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738187591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187591 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 9, 17, 17, 22, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 9, 9, 17, 49, 49, 49, 49, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 168 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738187591 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187591 Building ZINC001738187592 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738187592 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/634 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738187592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187592 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 8, 8, 12, 18, 18, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 12, 12, 18, 49, 49, 49, 49, 49, 49, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 167 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/635 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738187592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187592 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 2, 4, 11, 11, 19, 46, 47, 47, 47, 47, 47, 49, 49, 47, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 11, 47, 47, 47, 47, 49, 49, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738187592 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 Building ZINC001738187592 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738187592 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 634) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738187592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187592 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 8, 8, 12, 18, 18, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 12, 12, 18, 49, 49, 49, 49, 49, 49, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 167 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 635) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001738187592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738187592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738187592 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@](C)(CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 2, 4, 11, 11, 19, 46, 47, 47, 47, 47, 47, 49, 49, 47, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 11, 47, 47, 47, 47, 49, 49, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738187592 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738187592 Building ZINC001738206686 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738206686 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/636 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001738206686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738206686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738206686 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 9, 24, 24, 24, 45, 45, 45, 45, 45, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 9, 9, 24, 45, 45, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 7, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/637 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001738206686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738206686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738206686 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 3, 3, 8, 14, 31, 31, 31, 48, 48, 48, 48, 48, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 14, 14, 31, 48, 48, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738206686 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 Building ZINC001738206686 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738206686 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 636) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001738206686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738206686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738206686 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 9, 24, 24, 24, 45, 45, 45, 45, 45, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 9, 9, 24, 45, 45, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 7, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 637) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001738206686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738206686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738206686 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CCNC(=O)[C@H]2C[C@H]2C(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 3, 3, 8, 14, 31, 31, 31, 48, 48, 48, 48, 48, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 14, 14, 31, 48, 48, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738206686 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738206686 Building ZINC001738239353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738239353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/638 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738239353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738239353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239353 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 29, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/639 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738239353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738239353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239353 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 31, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738239353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 Building ZINC001738239353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738239353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 638) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738239353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738239353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239353 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 29, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 639) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738239353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738239353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239353 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 31, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738239353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239353 Building ZINC001738239356 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738239356 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/640 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738239356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738239356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239356 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 19, 33, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 33, 33, 43, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/641 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738239356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738239356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239356 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 20, 20, 34, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 34, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738239356 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 Building ZINC001738239356 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738239356 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 640) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738239356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738239356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239356 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 19, 33, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 33, 33, 43, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 641) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738239356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738239356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738239356 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 20, 20, 34, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 34, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738239356 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738239356 Building ZINC001738267860 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738267860 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/642 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738267860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738267860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267860 none CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 22, 22, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 22, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/643 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738267860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738267860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267860 none CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 12, 23, 23, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 23, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738267860 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 Building ZINC001738267860 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738267860 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 642) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738267860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738267860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267860 none CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 22, 22, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 22, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 643) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738267860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738267860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267860 none CC(C)C[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 12, 23, 23, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 23, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738267860 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267860 Building ZINC001738267861 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738267861 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/644 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738267861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738267861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267861 none CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 8, 2, 8, 8, 13, 21, 21, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 43, 43, 43, 43, 43, 43, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 170 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/645 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738267861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738267861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267861 none CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 13, 26, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 26, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738267861 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 Building ZINC001738267861 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738267861 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 644) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738267861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738267861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267861 none CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 8, 2, 8, 8, 13, 21, 21, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 43, 43, 43, 43, 43, 43, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 170 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 645) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738267861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738267861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738267861 none CC(C)C[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 13, 26, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 26, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738267861 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738267861 Building ZINC001738314927 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738314927 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/646 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738314927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314927 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 27, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 26, 26, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/647 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738314927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314927 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 23, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738314927 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 Building ZINC001738314927 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738314927 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 646) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738314927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314927 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 27, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 26, 26, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 647) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738314927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314927 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 23, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738314927 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314927 Building ZINC001738314928 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738314928 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/648 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738314928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314928 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 18, 18, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 17, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/649 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738314928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314928 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 22, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 23, 23, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738314928 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 Building ZINC001738314928 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738314928 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 648) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738314928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314928 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 18, 18, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 17, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 649) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001738314928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738314928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001738314928 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 22, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 23, 23, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738314928 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738314928 Building ZINC001738335521 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738335521 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/650 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738335521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738335521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335521 none CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 14, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 14, 14, 29, 45, 45, 45, 45, 45, 45, 45, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/651 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738335521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738335521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335521 none CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 5, 5, 12, 28, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 12, 12, 28, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738335521 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 Building ZINC001738335521 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738335521 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 650) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738335521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738335521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335521 none CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 14, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 14, 14, 29, 45, 45, 45, 45, 45, 45, 45, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 651) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738335521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738335521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335521 none CC(C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 5, 5, 12, 28, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 12, 12, 28, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738335521 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335521 Building ZINC001738335523 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738335523 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/652 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738335523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738335523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335523 none CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 15, 31, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 15, 15, 31, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/653 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738335523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738335523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335523 none CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 12, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 12, 12, 24, 40, 40, 40, 40, 40, 40, 40, 40, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738335523 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 Building ZINC001738335523 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738335523 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 652) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738335523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738335523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335523 none CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 15, 31, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 15, 15, 31, 49, 49, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 653) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738335523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738335523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001738335523 none CC(C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 12, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 12, 12, 24, 40, 40, 40, 40, 40, 40, 40, 40, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 57, 49, 50, 51, 52, 53, 22, 55, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738335523 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738335523 Building ZINC001638488428 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638488428 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/654 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/654' -> `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(c2nc(C)cc(O)n2)CC1) `ZINC001638488428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638488428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001638488428 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2nc(C)cc(O)n2)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 14, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 38, 38, 38, 38, 76, 14, 14, 14, 14] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/655 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/655' -> `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(c2nc(C)cc(O)n2)CC1) `ZINC001638488428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638488428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001638488428 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2nc(C)cc(O)n2)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 10, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 37, 37, 37, 37, 74, 15, 15, 15, 15] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638488428 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 Building ZINC001638488428 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638488428 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 654) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2nc(C)cc(O)n2)CC1) `ZINC001638488428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638488428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001638488428 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2nc(C)cc(O)n2)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 14, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 38, 38, 38, 38, 76, 14, 14, 14, 14] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 655) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2nc(C)cc(O)n2)CC1) `ZINC001638488428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638488428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001638488428 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2nc(C)cc(O)n2)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 10, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 37, 37, 37, 37, 74, 15, 15, 15, 15] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638488428 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638488428 Building ZINC001638645366 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638645366 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/656 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21) `ZINC001638645366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638645366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638645366 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 2, 3, 14, 14, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/657 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21) `ZINC001638645366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638645366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638645366 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 2, 3, 14, 14, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638645366 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 Building ZINC001638645366 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638645366 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 656) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21) `ZINC001638645366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638645366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638645366 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 2, 3, 14, 14, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 657) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21) `ZINC001638645366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638645366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638645366 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc2cc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 2, 3, 14, 14, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638645366 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638645366 Building ZINC001638656272 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638656272 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/658 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(COCCO)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638656272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638656272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638656272 none O=C(N1CCC(O)(COCCO)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 4, 4, 4, 4, 4, 4, 13, 24, 32, 32, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 13, 13, 32, 32, 32, 32, 96, 4, 4, 4, 4, 4, 4, 4, 4] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 222 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/659 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(COCCO)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638656272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638656272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638656272 none O=C(N1CCC(O)(COCCO)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 4, 4, 4, 4, 4, 4, 15, 24, 33, 34, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 15, 15, 33, 33, 34, 34, 102, 4, 4, 4, 4, 4, 4, 4, 4] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 246 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638656272 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 Building ZINC001638656272 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638656272 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 658) grep: /scratch/xiaobo/45881/xch-8058115.60/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: O=C(N1CCC(O)(COCCO)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638656272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638656272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638656272 none O=C(N1CCC(O)(COCCO)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 4, 4, 4, 4, 4, 4, 13, 24, 32, 32, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 13, 13, 32, 32, 32, 32, 96, 4, 4, 4, 4, 4, 4, 4, 4] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 222 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 659) grep: /scratch/xiaobo/45881/xch-8058115.60/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: O=C(N1CCC(O)(COCCO)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638656272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638656272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638656272 none O=C(N1CCC(O)(COCCO)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 4, 4, 4, 4, 4, 4, 15, 24, 33, 34, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 15, 15, 33, 33, 34, 34, 102, 4, 4, 4, 4, 4, 4, 4, 4] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 246 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638656272 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638656272 Building ZINC001738658359 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738658359 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/660 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001738658359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738658359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738658359 none CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 36, 29, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 42, 42, 42, 42, 42, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 36, 36, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/661 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001738658359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738658359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738658359 none CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 38, 30, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 42, 42, 42, 42, 42, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 38, 38, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738658359 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 Building ZINC001738658359 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738658359 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 660) grep: /scratch/xiaobo/45881/xch-8058115.60/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(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001738658359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738658359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738658359 none CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 36, 29, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 42, 42, 42, 42, 42, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 36, 36, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 661) grep: /scratch/xiaobo/45881/xch-8058115.60/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(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001738658359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738658359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001738658359 none CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 38, 30, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 42, 42, 42, 42, 42, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 38, 38, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738658359 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738658359 Building ZINC001738669778 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001738669778 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/662 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/663 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/664 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/664' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/665 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/665' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738669778 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 Building ZINC001738669778 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001738669778 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 662) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 663) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 664) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 665) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738669778 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 Building ZINC001738669778 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001738669778 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 662) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 663) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 664) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 665) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738669778 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 Building ZINC001738669778 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001738669778 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 662) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 663) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 50, 36, 36, 25, 23, 14, 8, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 25, 25, 23, 23, 8, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 664) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 665) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001738669778.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001738669778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001738669778 none CC[C@@H]1[C@@H](C(=O)NCCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 19, 10, 7, 4, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 19, 19, 7, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738669778 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738669778 Building ZINC001738694913 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738694913 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/666 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738694913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738694913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738694913 none CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 10, 11, 12, 12, 17, 17, 17, 39, 39, 39, 39, 39, 39, 50, 50, 39, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 10, 10, 12, 12, 12, 12, 17, 39, 39, 39, 39, 50, 50, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/667 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738694913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738694913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738694913 none CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 10, 12, 13, 14, 19, 19, 19, 39, 39, 39, 39, 39, 39, 50, 50, 39, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 10, 10, 13, 13, 14, 14, 19, 39, 39, 39, 39, 50, 50, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738694913 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 Building ZINC001738694913 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738694913 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 666) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001738694913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738694913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738694913 none CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 10, 11, 12, 12, 17, 17, 17, 39, 39, 39, 39, 39, 39, 50, 50, 39, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 10, 10, 12, 12, 12, 12, 17, 39, 39, 39, 39, 50, 50, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 667) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001738694913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738694913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738694913 none CN(CCOCCNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 10, 12, 13, 14, 19, 19, 19, 39, 39, 39, 39, 39, 39, 50, 50, 39, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 10, 10, 13, 13, 14, 14, 19, 39, 39, 39, 39, 50, 50, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738694913 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738694913 Building ZINC001454344387 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454344387 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/668 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F) `ZINC001454344387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001454344387 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 24, 25, 26, 27, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/669 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F) `ZINC001454344387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001454344387 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 24, 25, 26, 27, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454344387 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 Building ZINC001454344387 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454344387 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 668) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F) `ZINC001454344387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001454344387 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 24, 25, 26, 27, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 669) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F) `ZINC001454344387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001454344387 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 24, 25, 26, 27, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454344387 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454344387 Building ZINC001638753027 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638753027 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/670 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c1) `ZINC001638753027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638753027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638753027 none CCNS(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 35, 35, 35, 35, 35, 14, 35, 27, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 45, 45, 45, 45, 45, 41, 24, 35, 35, 14, 14, 2, 5, 5, 5, 5, 5, 35] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/671 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c1) `ZINC001638753027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638753027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638753027 none CCNS(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 14, 35, 27, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 46, 46, 46, 46, 46, 42, 14, 35, 35, 14, 14, 2, 5, 5, 5, 5, 5, 35] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638753027 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 Building ZINC001638753027 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638753027 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 670) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c1) `ZINC001638753027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638753027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638753027 none CCNS(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 35, 35, 35, 35, 35, 14, 35, 27, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 45, 45, 45, 45, 45, 41, 24, 35, 35, 14, 14, 2, 5, 5, 5, 5, 5, 35] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 671) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c1) `ZINC001638753027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638753027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638753027 none CCNS(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 14, 35, 27, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 46, 46, 46, 46, 46, 42, 14, 35, 35, 14, 14, 2, 5, 5, 5, 5, 5, 35] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638753027 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638753027 Building ZINC001556082074 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556082074 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/672 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001556082074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556082074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556082074 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 20, 20, 20, 5, 1, 1, 1, 1, 4, 4, 4, 10, 10, 9, 10, 10, 10, 10, 5, 5, 5, 5, 20, 20, 5, 4, 10, 10, 10, 20] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/673 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001556082074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556082074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556082074 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 20, 20, 20, 5, 1, 1, 1, 1, 4, 4, 4, 11, 11, 10, 11, 11, 11, 11, 5, 5, 5, 5, 20, 20, 5, 4, 11, 11, 11, 22] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556082074 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 Building ZINC001556082074 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556082074 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 672) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001556082074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556082074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556082074 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 20, 20, 20, 5, 1, 1, 1, 1, 4, 4, 4, 10, 10, 9, 10, 10, 10, 10, 5, 5, 5, 5, 20, 20, 5, 4, 10, 10, 10, 20] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 673) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001556082074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556082074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556082074 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 20, 20, 20, 5, 1, 1, 1, 1, 4, 4, 4, 11, 11, 10, 11, 11, 11, 11, 5, 5, 5, 5, 20, 20, 5, 4, 11, 11, 11, 22] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556082074 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556082074 Building ZINC001638780510 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638780510 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/674 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1) `ZINC001638780510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638780510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638780510 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 3, 7, 4, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/675 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1) `ZINC001638780510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638780510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638780510 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 12, 12, 12, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 3, 3, 3, 3, 12, 12, 12, 48, 48, 48, 48, 48, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638780510 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 Building ZINC001638780510 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638780510 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 674) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1) `ZINC001638780510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638780510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638780510 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 3, 7, 4, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 675) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1) `ZINC001638780510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638780510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638780510 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(n2cnc3c2nc(N)nc3N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 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, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 12, 12, 12, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 3, 3, 3, 3, 12, 12, 12, 48, 48, 48, 48, 48, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638780510 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638780510 Building ZINC001638781110 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638781110 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/676 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1) `ZINC001638781110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638781110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638781110 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 26, 26, 26, 26, 26, 5, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/677 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1) `ZINC001638781110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638781110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638781110 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 4, 4, 4, 4, 2, 4, 4, 6, 6, 6, 26, 26, 26, 26, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638781110 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 Building ZINC001638781110 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638781110 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 676) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1) `ZINC001638781110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638781110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638781110 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 26, 26, 26, 26, 26, 5, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 677) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1) `ZINC001638781110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638781110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001638781110 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(n3cnc4c3nc(N)nc4N)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 4, 4, 4, 4, 2, 4, 4, 6, 6, 6, 26, 26, 26, 26, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638781110 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638781110 Building ZINC001738800784 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738800784 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/678 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738800784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800784 none C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 26, 33, 47, 47, 47, 47, 47, 47, 50, 50, 47, 10, 10, 10, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 26, 27, 27, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/679 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738800784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800784 none C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 31, 33, 48, 48, 48, 48, 48, 48, 50, 50, 48, 7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 32, 32, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738800784 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 Building ZINC001738800784 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738800784 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 678) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738800784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800784 none C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 26, 33, 47, 47, 47, 47, 47, 47, 50, 50, 47, 10, 10, 10, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 26, 27, 27, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 679) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738800784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800784 none C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 31, 33, 48, 48, 48, 48, 48, 48, 50, 50, 48, 7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 32, 32, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738800784 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800784 Building ZINC001738800785 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738800785 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/680 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738800785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800785 none C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 32, 45, 45, 45, 45, 45, 45, 50, 50, 45, 7, 7, 7, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 27, 27, 28, 28, 45, 45, 45, 45, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/681 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738800785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800785 none C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 29, 35, 47, 47, 47, 47, 47, 47, 50, 50, 47, 10, 10, 10, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 29, 29, 30, 30, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738800785 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 Building ZINC001738800785 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738800785 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 680) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738800785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800785 none C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 32, 45, 45, 45, 45, 45, 45, 50, 50, 45, 7, 7, 7, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 27, 27, 28, 28, 45, 45, 45, 45, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 681) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001738800785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738800785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001738800785 none C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 29, 35, 47, 47, 47, 47, 47, 47, 50, 50, 47, 10, 10, 10, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 29, 29, 30, 30, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738800785 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738800785 Building ZINC001738870080 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738870080 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/682 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/682' -> `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](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738870080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870080 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 8, 8, 8, 8, 8, 8, 8, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 24, 8, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/683 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/683' -> `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](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738870080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870080 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 27, 9, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 159 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738870080 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 Building ZINC001738870080 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738870080 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 682) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738870080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870080 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 8, 8, 8, 8, 8, 8, 8, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 24, 8, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 683) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738870080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870080 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 27, 9, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 159 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738870080 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870080 Building ZINC001738870085 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738870085 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/684 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/684' -> `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](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738870085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870085 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 33, 11, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/685 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/685' -> `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](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738870085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870085 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 10, 10, 10, 10, 10, 10, 10, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 30, 10, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738870085 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 Building ZINC001738870085 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001738870085 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 684) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001738870085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870085 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 33, 11, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 685) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001738870085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001738870085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001738870085 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 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, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 10, 10, 10, 10, 10, 10, 10, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 30, 10, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001738870085 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001738870085 Building ZINC001556170251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556170251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/686 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2) `ZINC001556170251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556170251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556170251 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/687 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2) `ZINC001556170251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556170251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556170251 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 17, 17, 5, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556170251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 Building ZINC001556170251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556170251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 686) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2) `ZINC001556170251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556170251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556170251 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 687) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2) `ZINC001556170251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556170251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556170251 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 17, 17, 5, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556170251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556170251 Building ZINC001454443738 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454443738 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/688 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454443738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443738 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 18, 27, 27, 30, 30, 30, 30, 18, 18, 18, 10, 10, 21, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30, 30] 150 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/689 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454443738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443738 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 7, 4, 7, 7, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 23, 23, 28, 28, 28, 28, 17, 17, 17, 13, 13, 21, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454443738 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 Building ZINC001454443738 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454443738 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 688) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454443738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443738 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 18, 27, 27, 30, 30, 30, 30, 18, 18, 18, 10, 10, 21, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30, 30] 150 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 689) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454443738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443738 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 7, 4, 7, 7, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 23, 23, 28, 28, 28, 28, 17, 17, 17, 13, 13, 21, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454443738 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443738 Building ZINC001454443740 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454443740 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/690 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454443740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443740 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 7, 4, 7, 7, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 18, 24, 24, 28, 28, 28, 28, 18, 18, 18, 13, 13, 21, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/691 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454443740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443740 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 17, 26, 26, 29, 29, 29, 29, 17, 17, 17, 10, 10, 21, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454443740 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 Building ZINC001454443740 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454443740 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 690) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454443740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443740 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 7, 4, 7, 7, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 18, 24, 24, 28, 28, 28, 28, 18, 18, 18, 13, 13, 21, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 691) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C) `ZINC001454443740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454443740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001454443740 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', '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', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 17, 26, 26, 29, 29, 29, 29, 17, 17, 17, 10, 10, 21, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454443740 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454443740 Building ZINC001556267334 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556267334 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/692 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1) `ZINC001556267334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556267334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001556267334 none COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 50, 14, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 38, 38, 4, 3, 3, 6, 3, 3, 14, 14, 14, 14, 14, 14, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/693 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1) `ZINC001556267334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556267334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001556267334 none COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 50, 14, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 40, 40, 5, 3, 3, 6, 3, 3, 14, 14, 14, 14, 14, 14, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556267334 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 Building ZINC001556267334 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556267334 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 692) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1) `ZINC001556267334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556267334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001556267334 none COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 50, 14, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 38, 38, 4, 3, 3, 6, 3, 3, 14, 14, 14, 14, 14, 14, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 693) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1) `ZINC001556267334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556267334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001556267334 none COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCS(=O)(=O)CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 50, 14, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 40, 40, 5, 3, 3, 6, 3, 3, 14, 14, 14, 14, 14, 14, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556267334 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556267334 Building ZINC001638908582 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638908582 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/694 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001638908582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638908582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638908582 none CSc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 34, 34, 34, 24, 24, 10, 10, 2, 1, 4, 4, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [32, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 39, 40]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/695 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001638908582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638908582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638908582 none CSc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 23, 23, 31, 31, 31, 23, 23, 10, 10, 2, 1, 4, 4, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [32, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 39, 40]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638908582 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 Building ZINC001638908582 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638908582 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 694) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CSc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001638908582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638908582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638908582 none CSc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 34, 34, 34, 24, 24, 10, 10, 2, 1, 4, 4, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [32, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 39, 40]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 695) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CSc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001638908582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638908582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638908582 none CSc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 23, 23, 31, 31, 31, 23, 23, 10, 10, 2, 1, 4, 4, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [32, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 39, 40]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001638908582 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001638908582 Building ZINC001556312700 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001556312700 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/696 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/697 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 34, 34, 34, 34, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/698 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/698' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 13, 13, 13, 13, 6, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 32, 32, 32, 32, 13, 13, 3, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/699 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/699' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 32, 32, 32, 32, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556312700 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 Building ZINC001556312700 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001556312700 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 696) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 697) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 34, 34, 34, 34, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 698) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 13, 13, 13, 13, 6, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 32, 32, 32, 32, 13, 13, 3, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 699) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 32, 32, 32, 32, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556312700 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 Building ZINC001556312700 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001556312700 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 696) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 697) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 34, 34, 34, 34, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 698) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 13, 13, 13, 13, 6, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 32, 32, 32, 32, 13, 13, 3, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 699) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 32, 32, 32, 32, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556312700 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 Building ZINC001556312700 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001556312700 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 696) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 697) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 34, 34, 34, 34, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 698) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 13, 13, 13, 13, 6, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 32, 32, 32, 32, 13, 13, 3, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 699) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001556312700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001556312700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001556312700 none CS(=O)(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 32, 32, 32, 32, 14, 14, 3, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556312700 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556312700 Building ZINC001739064144 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739064144 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/700 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739064144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064144 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 13, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 23, 23, 23, 20, 20, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 231 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/701 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739064144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064144 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 38, 38, 42, 42, 42, 42, 42, 50, 50, 50, 50, 50, 25, 25, 25, 23, 23, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 237 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739064144 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 Building ZINC001739064144 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739064144 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 700) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739064144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064144 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 13, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 23, 23, 23, 20, 20, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 231 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 701) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739064144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064144 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 38, 38, 42, 42, 42, 42, 42, 50, 50, 50, 50, 50, 25, 25, 25, 23, 23, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 237 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739064144 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064144 Building ZINC001739064145 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739064145 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/702 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739064145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064145 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 17, 7, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 31, 31, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 22, 22, 22, 19, 19, 51, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 226 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/703 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739064145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064145 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 10, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 22, 22, 22, 16, 16, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739064145 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 Building ZINC001739064145 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739064145 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 702) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739064145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064145 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 17, 7, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 31, 31, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 22, 22, 22, 19, 19, 51, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 226 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 703) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C) `ZINC001739064145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739064145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739064145 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 10, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 22, 22, 22, 16, 16, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739064145 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739064145 Building ZINC001739066826 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739066826 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/704 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739066826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066826 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 35, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/705 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739066826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066826 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 22, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 34, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 22, 22, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 245 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739066826 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 Building ZINC001739066826 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739066826 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 704) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739066826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066826 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 35, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 705) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739066826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066826 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 22, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 34, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 22, 22, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 245 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739066826 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066826 Building ZINC001739066827 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739066827 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/706 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739066827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066827 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/707 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739066827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066827 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 33, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739066827 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 Building ZINC001739066827 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739066827 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 706) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739066827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066827 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 707) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001739066827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739066827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739066827 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 33, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739066827 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739066827 Building ZINC001556449704 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556449704 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/708 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556449704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449704 none O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/709 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556449704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449704 none O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556449704 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 Building ZINC001556449704 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556449704 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 708) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556449704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449704 none O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 709) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556449704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449704 none O=C(N1CCC[C@@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556449704 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449704 Building ZINC001556449705 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556449705 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/710 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556449705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449705 none O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/711 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556449705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449705 none O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556449705 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 Building ZINC001556449705 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556449705 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 710) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556449705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449705 none O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 711) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556449705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556449705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556449705 none O=C(N1CCC[C@]2(C1)NC(=O)NC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556449705 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556449705 Building ZINC001556467251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556467251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/712 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(=O)n(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O) `ZINC001556467251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556467251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001556467251 none Cn1ccc(=O)n(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 18, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 16, 16, 3, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/713 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(=O)n(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O) `ZINC001556467251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556467251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001556467251 none Cn1ccc(=O)n(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 18, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 16, 16, 3, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556467251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 Building ZINC001556467251 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556467251 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 712) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1ccc(=O)n(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O) `ZINC001556467251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556467251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001556467251 none Cn1ccc(=O)n(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 18, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 16, 16, 3, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 713) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1ccc(=O)n(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O) `ZINC001556467251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556467251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001556467251 none Cn1ccc(=O)n(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 18, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 16, 16, 3, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556467251 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556467251 Building ZINC001556517984 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556517984 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/714 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/714' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001556517984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556517984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556517984 none CN(C)S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 28, 33, 33, 17, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 28, 17, 17, 14, 14, 3, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/715 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/715' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001556517984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556517984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556517984 none CN(C)S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 28, 33, 33, 17, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 28, 17, 17, 14, 14, 3, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556517984 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 Building ZINC001556517984 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556517984 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 714) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556517984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556517984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556517984 none CN(C)S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 28, 33, 33, 17, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 28, 17, 17, 14, 14, 3, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 715) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001556517984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556517984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001556517984 none CN(C)S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 28, 33, 33, 17, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 28, 17, 17, 14, 14, 3, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556517984 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556517984 Building ZINC001639105773 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105773 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/716 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/717 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/718 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/718' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/719 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/719' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105773 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 Building ZINC001639105773 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105773 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 716) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 717) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 718) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 719) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105773 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 Building ZINC001639105773 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105773 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 716) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 717) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 718) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 719) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105773 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 Building ZINC001639105773 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105773 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 716) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 717) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 718) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 27, 27, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 3, 3, 1, 3, 3, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 719) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105773.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105773 none NC(=O)C1CC2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 28, 28, 28, 28, 28, 49, 49, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105773 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105773 Building ZINC001639105774 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105774 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/720 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/721 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/722 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/722' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/723 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/723' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105774 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 Building ZINC001639105774 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105774 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 720) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 721) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 722) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 723) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105774 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 Building ZINC001639105774 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105774 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 720) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 721) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 722) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 723) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105774 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 Building ZINC001639105774 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639105774 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 720) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 721) grep: /scratch/xiaobo/45881/xch-8058115.60/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: NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 722) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 27, 27, 27, 8, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 723) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O) `ZINC001639105774.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639105774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001639105774 none NC(=O)C1CC2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)CCS2(=O)=O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 28, 28, 28, 28, 28, 9, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 28, 50, 50, 28, 28, 28, 28, 28, 28, 28, 5, 3, 3, 1, 3, 3, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639105774 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639105774 Building ZINC001739366969 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739366969 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/724 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739366969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739366969 none CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 14, 5, 3, 5, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 29, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/725 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739366969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739366969 none CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 14, 8, 5, 8, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739366969 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 Building ZINC001739366969 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739366969 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 724) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739366969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739366969 none CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 14, 5, 3, 5, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 29, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 725) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739366969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739366969 none CCCC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 14, 8, 5, 8, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739366969 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366969 Building ZINC001739366974 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739366974 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/726 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739366974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739366974 none CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 27, 22, 6, 4, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 41, 41, 31, 31, 22, 22, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/727 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739366974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739366974 none CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 41, 40, 28, 28, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739366974 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 Building ZINC001739366974 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739366974 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 726) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739366974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739366974 none CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 27, 22, 6, 4, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 41, 41, 31, 31, 22, 22, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 727) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739366974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739366974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739366974 none CC(=O)N(C)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 41, 40, 28, 28, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739366974 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739366974 Building ZINC001739367407 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739367407 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/728 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739367407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367407 none CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 21, 31, 19, 10, 7, 10, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 31, 21, 21, 19, 19, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/729 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739367407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367407 none CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 29, 29, 21, 29, 17, 9, 6, 9, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 29, 21, 21, 17, 17, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739367407 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 Building ZINC001739367407 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739367407 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 728) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739367407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367407 none CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 21, 31, 19, 10, 7, 10, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 31, 21, 21, 19, 19, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 729) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739367407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367407 none CCCNC(=O)CCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 29, 29, 21, 29, 17, 9, 6, 9, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 29, 21, 21, 17, 17, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739367407 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367407 Building ZINC001739367854 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739367854 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/730 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739367854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367854 none CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 26, 43, 10, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 26, 26, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/731 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739367854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367854 none CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 50, 22, 39, 7, 6, 7, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739367854 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 Building ZINC001739367854 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739367854 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 730) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739367854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367854 none CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 26, 43, 10, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 26, 26, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 731) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001739367854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739367854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739367854 none CC(C)C(=O)N(C)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 50, 22, 39, 7, 6, 7, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739367854 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367854 Building ZINC001739367892 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739367892 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/732 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21) `ZINC001739367892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739367892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739367892 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 5, 5, 15, 28, 28, 33, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 15, 15, 28, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/733 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21) `ZINC001739367892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739367892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739367892 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 16, 28, 28, 33, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 16, 16, 28, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739367892 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 Building ZINC001739367892 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739367892 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 732) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21) `ZINC001739367892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739367892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739367892 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 5, 5, 15, 28, 28, 33, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 15, 15, 28, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 733) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21) `ZINC001739367892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739367892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739367892 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CNC(=O)C3CCC3)C[C@H]21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 16, 28, 28, 33, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 16, 16, 28, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739367892 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739367892 Building ZINC001739392732 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739392732 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/734 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001739392732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739392732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739392732 none COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 26, 19, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 39, 39, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/735 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001739392732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739392732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739392732 none COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 26, 20, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 37, 37, 26, 26, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739392732 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 Building ZINC001739392732 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739392732 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 734) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001739392732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739392732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739392732 none COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 26, 19, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 39, 39, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 735) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001739392732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739392732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739392732 none COCCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 26, 20, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 37, 37, 26, 26, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739392732 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739392732 Building ZINC001556656663 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556656663 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/736 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556656663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656663 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 47, 12, 47, 12, 12, 21, 21, 12, 12, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 49, 49, 49, 49, 49, 21, 21, 21, 12, 12, 12, 12, 1, 1, 2, 1, 1, 12, 12, 12, 12] 100 rigid atoms, others: [37, 38, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 42, 43, 44, 45]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/737 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556656663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656663 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 48, 13, 48, 13, 13, 20, 20, 13, 13, 5, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 13, 13, 2, 2, 4, 2, 2, 13, 13, 13, 13] 100 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556656663 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 Building ZINC001556656663 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556656663 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 736) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556656663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656663 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 47, 12, 47, 12, 12, 21, 21, 12, 12, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 49, 49, 49, 49, 49, 21, 21, 21, 12, 12, 12, 12, 1, 1, 2, 1, 1, 12, 12, 12, 12] 100 rigid atoms, others: [37, 38, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 42, 43, 44, 45]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 737) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556656663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656663 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 48, 13, 48, 13, 13, 20, 20, 13, 13, 5, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 13, 13, 2, 2, 4, 2, 2, 13, 13, 13, 13] 100 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556656663 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656663 Building ZINC001556656664 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556656664 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/738 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556656664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656664 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 47, 10, 47, 10, 10, 19, 19, 10, 10, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 19, 19, 19, 10, 10, 10, 10, 1, 1, 2, 1, 1, 10, 10, 10, 10] 100 rigid atoms, others: [37, 38, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/739 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556656664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656664 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 47, 14, 47, 14, 14, 22, 22, 14, 14, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 14, 14, 1, 1, 2, 1, 1, 14, 14, 14, 14] 100 rigid atoms, others: [37, 38, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556656664 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 Building ZINC001556656664 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556656664 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 738) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556656664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656664 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 47, 10, 47, 10, 10, 19, 19, 10, 10, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 19, 19, 19, 10, 10, 10, 10, 1, 1, 2, 1, 1, 10, 10, 10, 10] 100 rigid atoms, others: [37, 38, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 739) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001556656664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556656664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001556656664 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', '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', '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, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 47, 14, 47, 14, 14, 22, 22, 14, 14, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 14, 14, 1, 1, 2, 1, 1, 14, 14, 14, 14] 100 rigid atoms, others: [37, 38, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556656664 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556656664 Building ZINC001739408862 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739408862 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/740 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001739408862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739408862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739408862 none CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 31, 19, 7, 19, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 31, 50, 50, 50, 50, 50, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/741 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001739408862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739408862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739408862 none CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 21, 8, 21, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 32, 50, 50, 50, 50, 50, 32, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 32, 32, 32] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739408862 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 Building ZINC001739408862 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739408862 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 740) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001739408862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739408862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739408862 none CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 31, 19, 7, 19, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 31, 50, 50, 50, 50, 50, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 741) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001739408862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739408862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739408862 none CCn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 21, 8, 21, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 32, 50, 50, 50, 50, 50, 32, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 32, 32, 32] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739408862 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739408862 Building ZINC001739409211 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409211 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/742 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O) `ZINC001739409211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739409211 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 14, 14, 32, 50, 50, 44, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 44, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 283 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/743 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O) `ZINC001739409211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739409211 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 14, 14, 34, 50, 50, 44, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 34, 34, 44, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409211 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 Building ZINC001739409211 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409211 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 742) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O) `ZINC001739409211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739409211 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 14, 14, 32, 50, 50, 44, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 44, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 283 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 743) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O) `ZINC001739409211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739409211 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(F)(F)C(F)F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 14, 14, 34, 50, 50, 44, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 34, 34, 44, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409211 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409211 Building ZINC001739409258 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409258 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/744 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O) `ZINC001739409258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739409258 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 4, 10, 10, 10, 10, 17, 17, 40, 40, 40, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 40, 40, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 235 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/745 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O) `ZINC001739409258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739409258 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 21, 21, 39, 39, 39, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 229 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409258 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 Building ZINC001739409258 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409258 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 744) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O) `ZINC001739409258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739409258 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 4, 10, 10, 10, 10, 17, 17, 40, 40, 40, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 40, 40, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 235 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 745) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O) `ZINC001739409258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739409258 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)C2CCOCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 21, 21, 39, 39, 39, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 229 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409258 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409258 Building ZINC001739409287 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409287 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/746 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409287 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 48, 48, 27, 9, 27, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/747 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409287 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 47, 47, 47, 47, 47, 47, 28, 11, 28, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409287 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 Building ZINC001739409287 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409287 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 746) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409287 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 48, 48, 27, 9, 27, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 747) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409287 none CCc1[nH]nc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 6, 8, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 47, 47, 47, 47, 47, 47, 28, 11, 28, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409287 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409287 Building ZINC001739409445 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409445 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/748 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409445 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 24, 8, 24, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 45, 45, 45, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/749 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409445 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 42, 50, 50, 23, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 42, 42, 42, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409445 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 Building ZINC001739409445 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409445 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 748) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409445 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 24, 8, 24, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 45, 45, 45, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 749) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409445 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 42, 50, 50, 23, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 42, 42, 42, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409445 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409445 Building ZINC001739409449 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409449 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/750 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409449 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 17, 9, 17, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 48, 48, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/751 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409449 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 17, 11, 17, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 47, 47, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409449 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 Building ZINC001739409449 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409449 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 750) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409449 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 17, 9, 17, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 48, 48, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 751) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409449 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 17, 11, 17, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 47, 47, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409449 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409449 Building ZINC001739409450 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409450 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/752 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409450 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 17, 9, 17, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 49, 49, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/753 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409450 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 15, 9, 15, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 49, 49, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 216 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409450 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 Building ZINC001739409450 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409450 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 752) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409450 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 17, 9, 17, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 49, 49, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 753) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F) `ZINC001739409450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409450 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 15, 9, 15, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 49, 49, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 216 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409450 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409450 Building ZINC001739409473 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409473 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/754 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/755 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/756 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/756' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/757 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/757' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409473 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 Building ZINC001739409473 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409473 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 754) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 755) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 756) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 757) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409473 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 Building ZINC001739409473 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409473 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 754) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 755) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 756) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 757) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409473 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 Building ZINC001739409473 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409473 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 754) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 755) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 756) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 50, 35, 16, 10, 16, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 35, 35, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 757) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409473 none CN1CCC[C@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409473 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409473 Building ZINC001739409474 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409474 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/758 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/759 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/760 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/760' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/761 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/761' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409474 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 Building ZINC001739409474 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409474 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 758) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 759) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 760) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 761) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409474 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 Building ZINC001739409474 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409474 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 758) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 759) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 760) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 761) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409474 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 Building ZINC001739409474 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409474 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 758) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 759) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 760) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 761) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409474 none CN1CCC[C@@H]1CCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 50, 35, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409474 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409474 Building ZINC001739409510 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409510 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/762 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/763 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/764 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/764' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/765 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/765' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409510 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 Building ZINC001739409510 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409510 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 762) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 763) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 764) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 765) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409510 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 Building ZINC001739409510 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409510 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 762) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 763) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 764) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 765) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409510 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 Building ZINC001739409510 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409510 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 762) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 763) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 764) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 765) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409510.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409510 none CC(C)N1CCC[C@@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409510 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409510 Building ZINC001739409511 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409511 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/766 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/767 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/768 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/768' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/769 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/769' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409511 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 Building ZINC001739409511 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409511 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 766) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 767) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 768) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 769) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409511 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 Building ZINC001739409511 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409511 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 766) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 767) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 768) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 769) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409511 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 Building ZINC001739409511 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409511 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 766) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 767) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 14, 22, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 768) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 769) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409511.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409511 none CC(C)N1CCC[C@H]1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 16, 22, 16, 16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 16, 16, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 227 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409511 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409511 Building ZINC001739409529 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409529 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/770 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409529 none C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 29, 44, 9, 29, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 50, 50, 50, 44, 44, 44, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/771 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409529 none C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 32, 43, 11, 32, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 45, 50, 50, 50, 50, 50, 43, 43, 43, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409529 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 Building ZINC001739409529 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409529 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 770) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409529 none C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 29, 44, 9, 29, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 50, 50, 50, 44, 44, 44, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 771) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409529 none C[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 32, 43, 11, 32, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 45, 50, 50, 50, 50, 50, 43, 43, 43, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409529 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409529 Building ZINC001739409530 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409530 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/772 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409530 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 28, 42, 10, 28, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 50, 50, 50, 50, 50, 42, 42, 42, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/773 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409530 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 40, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 50, 50, 50, 50, 50, 40, 40, 40, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409530 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 Building ZINC001739409530 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409530 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 772) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409530 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 28, 42, 10, 28, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 50, 50, 50, 50, 50, 42, 42, 42, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 773) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1) `ZINC001739409530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739409530 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 40, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 50, 50, 50, 50, 50, 40, 40, 40, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409530 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409530 Building ZINC001739409638 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409638 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/774 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409638 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/775 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409638 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 17, 8, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409638 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 Building ZINC001739409638 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409638 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 774) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409638 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 775) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409638 none CC[C@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 17, 8, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409638 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409638 Building ZINC001739409639 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409639 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/776 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409639 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 50, 42, 42, 42, 42, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/777 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409639 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409639 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 Building ZINC001739409639 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409639 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 776) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409639 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 50, 42, 42, 42, 42, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 777) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739409639 none CC[C@@H](C)n1nccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 50, 43, 43, 43, 43, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409639 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409639 Building ZINC001739409666 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409666 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/778 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739409666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409666 none CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 46, 46, 46, 20, 9, 20, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 50, 50, 50, 50, 50, 46, 46, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/779 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739409666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409666 none CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 46, 46, 46, 22, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 46, 50, 50, 50, 50, 50, 50, 50, 46, 46, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409666 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 Building ZINC001739409666 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409666 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 778) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739409666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409666 none CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 46, 46, 46, 20, 9, 20, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 50, 50, 50, 50, 50, 46, 46, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 779) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739409666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409666 none CC(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 46, 46, 46, 22, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 46, 50, 50, 50, 50, 50, 50, 50, 46, 46, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409666 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409666 Building ZINC001739409675 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409675 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/780 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O) `ZINC001739409675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409675 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 17, 17, 42, 42, 42, 42, 50, 50, 42, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/781 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O) `ZINC001739409675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409675 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 9, 9, 9, 9, 17, 17, 46, 46, 46, 46, 50, 50, 46, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 46, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409675 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 Building ZINC001739409675 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409675 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 780) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O) `ZINC001739409675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409675 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 17, 17, 42, 42, 42, 42, 50, 50, 42, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 781) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O) `ZINC001739409675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409675 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc(C3CC3)s2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 9, 9, 9, 9, 17, 17, 46, 46, 46, 46, 50, 50, 46, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 46, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409675 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409675 Building ZINC001739409728 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409728 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/782 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/783 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/784 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/784' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 6, 6, 10, 10, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/785 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/785' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 40, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409728 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 Building ZINC001739409728 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409728 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 782) grep: /scratch/xiaobo/45881/xch-8058115.60/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)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 783) grep: /scratch/xiaobo/45881/xch-8058115.60/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)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 784) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 6, 6, 10, 10, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 785) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 40, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409728 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 Building ZINC001739409728 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409728 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 782) grep: /scratch/xiaobo/45881/xch-8058115.60/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)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 783) grep: /scratch/xiaobo/45881/xch-8058115.60/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)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 784) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 6, 6, 10, 10, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 785) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 40, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409728 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 Building ZINC001739409728 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409728 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 782) grep: /scratch/xiaobo/45881/xch-8058115.60/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)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 39, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 783) grep: /scratch/xiaobo/45881/xch-8058115.60/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)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 784) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 6, 6, 10, 10, 39, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 785) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O) `ZINC001739409728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409728 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC[N@@](C)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 11, 11, 40, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409728 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409728 Building ZINC001739409729 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409729 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/786 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O) `ZINC001739409729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409729 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 16, 16, 38, 38, 38, 38, 38, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 38, 38, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/787 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O) `ZINC001739409729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409729 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 14, 14, 35, 35, 35, 35, 36, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 35, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409729 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 Building ZINC001739409729 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409729 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 786) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O) `ZINC001739409729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409729 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 16, 16, 38, 38, 38, 38, 38, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 38, 38, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 787) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O) `ZINC001739409729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409729 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 14, 14, 35, 35, 35, 35, 36, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 35, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409729 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409729 Building ZINC001739409850 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409850 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/788 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O) `ZINC001739409850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409850 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 15, 15, 15, 15, 27, 27, 48, 48, 48, 48, 48, 48, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 48, 48, 48, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/789 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O) `ZINC001739409850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409850 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 26, 26, 48, 48, 48, 48, 48, 48, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 48, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409850 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 Building ZINC001739409850 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409850 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 788) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O) `ZINC001739409850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409850 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 15, 15, 15, 15, 27, 27, 48, 48, 48, 48, 48, 48, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 48, 48, 48, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 789) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O) `ZINC001739409850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739409850 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 26, 26, 48, 48, 48, 48, 48, 48, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 48, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409850 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409850 Building ZINC001739409916 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409916 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/790 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001739409916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409916 none Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 50, 50, 26, 15, 6, 4, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 26, 50, 50, 15, 15, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/791 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001739409916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409916 none Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 50, 50, 28, 16, 7, 5, 7, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 28, 50, 50, 16, 16, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409916 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 Building ZINC001739409916 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409916 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 790) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001739409916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409916 none Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 50, 50, 26, 15, 6, 4, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 26, 50, 50, 15, 15, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 791) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001739409916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739409916 none Cc1cccc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 50, 50, 28, 16, 7, 5, 7, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 28, 50, 50, 16, 16, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409916 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409916 Building ZINC001739409923 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409923 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/792 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/793 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/794 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/794' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/795 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/795' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409923 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 Building ZINC001739409923 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409923 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 792) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 793) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 794) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 795) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409923 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 Building ZINC001739409923 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409923 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 792) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 793) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 794) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 795) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409923 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 Building ZINC001739409923 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409923 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 792) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 793) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 15, 31, 7, 15, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 794) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 795) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409923.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409923 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 17, 33, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409923 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409923 Building ZINC001739409924 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409924 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/796 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/797 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/798 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/798' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/799 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/799' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409924 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 Building ZINC001739409924 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409924 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 796) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 797) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 798) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 799) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409924 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 Building ZINC001739409924 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409924 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 796) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 797) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 798) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 799) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409924 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 Building ZINC001739409924 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409924 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 796) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 797) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 17, 35, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 798) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 799) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001739409924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739409924 none CCCN1CCC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 17, 34, 9, 17, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409924 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409924 Building ZINC001739409928 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409928 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/800 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O) `ZINC001739409928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409928 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/801 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O) `ZINC001739409928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409928 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409928 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 Building ZINC001739409928 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409928 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 800) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O) `ZINC001739409928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409928 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 801) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O) `ZINC001739409928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739409928 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nccn3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409928 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409928 Building ZINC001739409976 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409976 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/802 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)sc1C) `ZINC001739409976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409976 none Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 22, 8, 22, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/803 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)sc1C) `ZINC001739409976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409976 none Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 25, 12, 25, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409976 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 Building ZINC001739409976 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739409976 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 802) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)sc1C) `ZINC001739409976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409976 none Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 22, 8, 22, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 803) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)sc1C) `ZINC001739409976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739409976 none Cc1nc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 25, 12, 25, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409976 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409976 Building ZINC001739409987 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409987 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/804 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/805 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/806 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/806' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/807 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/807' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409987 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 Building ZINC001739409987 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409987 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 804) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 805) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 806) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 807) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409987 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 Building ZINC001739409987 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409987 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 804) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 805) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 806) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 807) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409987 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 Building ZINC001739409987 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409987 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 804) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 805) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 17, 38, 7, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 806) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 807) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409987.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409987 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 18, 37, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409987 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409987 Building ZINC001739409989 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409989 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/808 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/809 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/810 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/810' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/811 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/811' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409989 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 Building ZINC001739409989 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409989 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 808) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 809) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 810) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 811) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409989 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 Building ZINC001739409989 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409989 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 808) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 809) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 810) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 811) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409989 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 Building ZINC001739409989 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739409989 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 808) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 809) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 42, 19, 42, 9, 19, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 810) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 811) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739409989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739409989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739409989 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 19, 37, 11, 19, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739409989 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739409989 Building ZINC001739410052 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410052 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/812 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410052 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 14, 14, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/813 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410052 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 15, 15, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410052 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 Building ZINC001739410052 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410052 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 812) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410052 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 14, 14, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 813) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410052 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 15, 15, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410052 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410052 Building ZINC001739410055 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410055 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/814 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410055 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 16, 16, 43, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/815 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410055 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 16, 16, 42, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410055 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 Building ZINC001739410055 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410055 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 814) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410055 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 16, 16, 43, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 815) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O) `ZINC001739410055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739410055 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(C)(C)CO2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 16, 16, 42, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410055 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410055 Building ZINC001739410098 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410098 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/816 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O) `ZINC001739410098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739410098 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 18, 18, 18, 18, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/817 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O) `ZINC001739410098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739410098 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 18, 18, 18, 18, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410098 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 Building ZINC001739410098 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410098 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 816) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O) `ZINC001739410098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739410098 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 18, 18, 18, 18, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 817) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O) `ZINC001739410098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739410098 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3c2CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 18, 18, 18, 18, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410098 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410098 Building ZINC001739410165 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410165 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/818 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O) `ZINC001739410165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739410165 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 15, 15, 15, 15, 26, 26, 49, 49, 49, 49, 49, 49, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 49, 49, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/819 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O) `ZINC001739410165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739410165 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 23, 23, 45, 45, 45, 45, 45, 45, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 45, 45, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410165 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 Building ZINC001739410165 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410165 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 818) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O) `ZINC001739410165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739410165 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 15, 15, 15, 15, 26, 26, 49, 49, 49, 49, 49, 49, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 49, 49, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 819) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O) `ZINC001739410165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739410165 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncnc2C2CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 23, 23, 45, 45, 45, 45, 45, 45, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 45, 45, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410165 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410165 Building ZINC001739410184 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410184 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/820 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001739410184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410184 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 9, 23, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/821 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001739410184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410184 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 11, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410184 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 Building ZINC001739410184 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410184 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 820) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001739410184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410184 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 9, 23, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 821) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001739410184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410184 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 11, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410184 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410184 Building ZINC001739410209 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410209 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/822 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/823 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/824 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/824' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/825 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/825' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410209 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 Building ZINC001739410209 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410209 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 822) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 823) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 824) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 825) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410209 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 Building ZINC001739410209 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410209 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 822) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 823) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 824) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 825) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410209 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 Building ZINC001739410209 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410209 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 822) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 823) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 50, 8, 21, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 165 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 824) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 825) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410209 none CC(C)CN1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 9, 23, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410209 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410209 Building ZINC001739410210 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410210 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/826 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/827 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/828 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/828' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/829 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/829' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410210 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 Building ZINC001739410210 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410210 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 826) grep: /scratch/xiaobo/45881/xch-8058115.60/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(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 827) grep: /scratch/xiaobo/45881/xch-8058115.60/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(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 828) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 829) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410210 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 Building ZINC001739410210 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410210 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 826) grep: /scratch/xiaobo/45881/xch-8058115.60/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(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 827) grep: /scratch/xiaobo/45881/xch-8058115.60/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(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 828) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 829) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410210 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 Building ZINC001739410210 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739410210 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 826) grep: /scratch/xiaobo/45881/xch-8058115.60/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(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 827) grep: /scratch/xiaobo/45881/xch-8058115.60/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(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 50, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 828) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 829) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001739410210.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739410210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739410210 none CC(C)CN1CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410210 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410210 Building ZINC001739410295 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410295 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/830 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O) `ZINC001739410295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739410295 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/831 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O) `ZINC001739410295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739410295 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410295 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 Building ZINC001739410295 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410295 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 830) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O) `ZINC001739410295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739410295 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 831) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O) `ZINC001739410295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739410295 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3ccccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410295 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410295 Building ZINC001739410320 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410320 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/832 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410320 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 31, 36, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 50, 50, 36, 36, 36, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/833 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410320 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 36, 13, 9, 13, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 36, 50, 50, 50, 50, 50, 36, 36, 36, 32, 32, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410320 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 Building ZINC001739410320 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410320 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 832) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410320 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 31, 36, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 50, 50, 36, 36, 36, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 833) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410320 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 36, 13, 9, 13, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 36, 50, 50, 50, 50, 50, 36, 36, 36, 32, 32, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410320 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410320 Building ZINC001739410321 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410321 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/834 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410321 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens 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, 32, 37, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 37, 50, 50, 50, 50, 50, 37, 37, 37, 32, 32, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/835 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410321 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 36, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 50, 50, 36, 36, 36, 32, 32, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410321 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 Building ZINC001739410321 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410321 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 834) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410321 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens 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, 32, 37, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 37, 50, 50, 50, 50, 50, 37, 37, 37, 32, 32, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 835) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001739410321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410321 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 36, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 50, 50, 36, 36, 36, 32, 32, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410321 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410321 Building ZINC001739410330 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410330 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/836 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410330 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 3, 11, 11, 11, 11, 32, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/837 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410330 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 12, 12, 12, 12, 30, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410330 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 Building ZINC001739410330 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410330 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 836) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410330 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 3, 11, 11, 11, 11, 32, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 837) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410330 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 12, 12, 12, 12, 30, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410330 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410330 Building ZINC001739410331 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410331 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/838 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410331 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 12, 12, 12, 12, 29, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/839 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410331 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410331 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 Building ZINC001739410331 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410331 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 838) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410331 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 12, 12, 12, 12, 29, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 839) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O) `ZINC001739410331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739410331 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3c[nH]nc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410331 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410331 Building ZINC001739410371 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410371 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/840 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410371 none Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 26, 15, 26, 26, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 43, 43, 26, 26, 26, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/841 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410371 none Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 28, 16, 28, 28, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 43, 43, 28, 28, 28, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410371 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 Building ZINC001739410371 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410371 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 840) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410371 none Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 26, 15, 26, 26, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 43, 43, 26, 26, 26, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 841) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410371 none Cc1ccn(C[C@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 28, 16, 28, 28, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 43, 43, 28, 28, 28, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410371 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410371 Building ZINC001739410372 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410372 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/842 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410372 none Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 26, 12, 26, 26, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 43, 43, 26, 26, 26, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/843 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410372 none Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 28, 16, 28, 28, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 44, 44, 28, 28, 28, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 226 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410372 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 Building ZINC001739410372 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739410372 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 842) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739410372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410372 none Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 26, 12, 26, 26, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 43, 43, 26, 26, 26, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 843) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001739410372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739410372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739410372 none Cc1ccn(C[C@@H](C)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 28, 16, 28, 28, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 44, 44, 28, 28, 28, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 226 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739410372 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739410372 Building ZINC001739422277 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739422277 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/844 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739422277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739422277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739422277 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 22, 19, 5, 5, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 31, 31, 27, 27, 19, 19, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/845 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739422277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739422277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739422277 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 21, 19, 5, 5, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 31, 30, 27, 27, 19, 19, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739422277 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 Building ZINC001739422277 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739422277 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 844) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739422277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739422277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739422277 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 22, 19, 5, 5, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 31, 31, 27, 27, 19, 19, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 845) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739422277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739422277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739422277 none Cc1noc(CCCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 21, 19, 5, 5, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 31, 30, 27, 27, 19, 19, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739422277 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739422277 Building ZINC001739431617 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739431617 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/846 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1) `ZINC001739431617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739431617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739431617 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 3, 4, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 40, 47, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 40, 40, 47, 47, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/847 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1) `ZINC001739431617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739431617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739431617 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 4, 7, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 43, 45, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 16, 43, 43, 45, 45, 50, 50, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739431617 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 Building ZINC001739431617 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739431617 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 846) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1) `ZINC001739431617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739431617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739431617 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 3, 4, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 40, 47, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 40, 40, 47, 47, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 847) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1) `ZINC001739431617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739431617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739431617 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 4, 7, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 43, 45, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 16, 43, 43, 45, 45, 50, 50, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739431617 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431617 Building ZINC001739431668 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739431668 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/848 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1) `ZINC001739431668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739431668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739431668 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 22, 31, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 17, 17, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 56, 57] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/849 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1) `ZINC001739431668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739431668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739431668 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 17, 21, 32, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 3, 17, 17, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 7, 36, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739431668 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 Building ZINC001739431668 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739431668 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 848) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1) `ZINC001739431668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739431668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739431668 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 22, 31, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 17, 17, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 56, 57] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 849) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1) `ZINC001739431668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739431668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739431668 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 17, 21, 32, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 3, 17, 17, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 7, 36, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739431668 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739431668 Building ZINC001556687381 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556687381 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/850 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001556687381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556687381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001556687381 none COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 1, 1, 1, 1, 5, 8, 14, 5, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 4, 4, 19, 37, 42, 42, 42, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 4, 4, 19, 19, 37, 42, 42, 42, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/851 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001556687381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556687381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001556687381 none COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 1, 1, 1, 1, 5, 8, 14, 5, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 3, 4, 4, 17, 34, 39, 39, 39, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 4, 4, 17, 17, 34, 39, 39, 39, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556687381 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 Building ZINC001556687381 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556687381 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 850) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001556687381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556687381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001556687381 none COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 1, 1, 1, 1, 5, 8, 14, 5, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 4, 4, 19, 37, 42, 42, 42, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 4, 4, 19, 19, 37, 42, 42, 42, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 851) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001556687381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556687381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001556687381 none COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 1, 1, 1, 1, 5, 8, 14, 5, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 3, 4, 4, 17, 34, 39, 39, 39, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 4, 4, 17, 17, 34, 39, 39, 39, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556687381 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556687381 Building ZINC001739435871 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739435871 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/852 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001739435871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739435871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739435871 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 11, 11, 11, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/853 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001739435871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739435871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739435871 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 10, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739435871 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 Building ZINC001739435871 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739435871 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 852) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001739435871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739435871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739435871 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 11, 11, 11, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 853) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001739435871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739435871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739435871 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 10, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739435871 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739435871 Building ZINC001556698566 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556698566 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/854 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1) `ZINC001556698566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556698566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556698566 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/855 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1) `ZINC001556698566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556698566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556698566 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556698566 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 Building ZINC001556698566 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556698566 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 854) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1) `ZINC001556698566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556698566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556698566 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 855) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1) `ZINC001556698566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556698566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556698566 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc2nc[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556698566 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556698566 Building ZINC001739447332 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739447332 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/856 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739447332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739447332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739447332 none Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 13, 13, 13, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 40, 40, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/857 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739447332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739447332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739447332 none Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 39, 36, 14, 14, 14, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 36, 36, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739447332 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 Building ZINC001739447332 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739447332 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 856) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739447332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739447332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739447332 none Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 13, 13, 13, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 40, 40, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 857) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001739447332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739447332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739447332 none Cc1cc(C)n(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 39, 36, 14, 14, 14, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 36, 36, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739447332 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739447332 Building ZINC001639263117 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639263117 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/858 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21) `ZINC001639263117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639263117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001639263117 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21 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', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/859 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21) `ZINC001639263117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639263117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001639263117 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21 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', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639263117 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 Building ZINC001639263117 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639263117 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 858) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21) `ZINC001639263117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639263117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001639263117 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21 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', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 859) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21) `ZINC001639263117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639263117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001639263117 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nnc2ccc(N(C)C)nn21 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', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639263117 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639263117 Building ZINC001739470601 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739470601 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/860 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1) `ZINC001739470601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739470601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739470601 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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] 1 hydrogens 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, 3, 4, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 48, 50, 50, 42, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 19, 48, 48, 45, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/861 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1) `ZINC001739470601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739470601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739470601 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 7, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 47, 50, 50, 39, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 19, 47, 47, 40, 9, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739470601 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 Building ZINC001739470601 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739470601 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 860) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1) `ZINC001739470601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739470601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739470601 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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] 1 hydrogens 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, 3, 4, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 48, 50, 50, 42, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 19, 48, 48, 45, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 861) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1) `ZINC001739470601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739470601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001739470601 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CC(F)(F)C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 7, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 47, 50, 50, 39, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 19, 47, 47, 40, 9, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739470601 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739470601 Building ZINC001454783999 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454783999 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/862 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1) `ZINC001454783999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454783999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454783999 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 13, 13, 13, 13, 13, 14, 14, 14, 19, 13, 13, 6, 6, 12, 12, 12, 12, 12, 6, 2, 11, 11, 13, 13, 13, 13, 19, 19, 19, 19, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/863 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1) `ZINC001454783999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454783999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454783999 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 13, 13, 13, 13, 13, 14, 14, 14, 19, 13, 13, 6, 6, 12, 12, 12, 12, 12, 6, 2, 11, 11, 13, 13, 13, 13, 19, 19, 19, 19, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454783999 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 Building ZINC001454783999 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454783999 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 862) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1) `ZINC001454783999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454783999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454783999 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 13, 13, 13, 13, 13, 14, 14, 14, 19, 13, 13, 6, 6, 12, 12, 12, 12, 12, 6, 2, 11, 11, 13, 13, 13, 13, 19, 19, 19, 19, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 863) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1) `ZINC001454783999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454783999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454783999 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)NC)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 13, 13, 13, 13, 13, 14, 14, 14, 19, 13, 13, 6, 6, 12, 12, 12, 12, 12, 6, 2, 11, 11, 13, 13, 13, 13, 19, 19, 19, 19, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001454783999 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001454783999 Building ZINC001739497100 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497100 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/864 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497100 none COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 28, 12, 28, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/865 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497100 none COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 28, 13, 28, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497100 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 Building ZINC001739497100 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497100 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 864) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497100 none COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 28, 12, 28, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 865) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497100 none COC[C@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 28, 13, 28, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497100 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497100 Building ZINC001739497101 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497101 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/866 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497101 none COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 30, 13, 30, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/867 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497101 none COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 29, 15, 29, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 36, 36, 36, 36, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497101 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 Building ZINC001739497101 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497101 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 866) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497101 none COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 30, 13, 30, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 867) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1) `ZINC001739497101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739497101 none COC[C@@]1(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 29, 15, 29, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 36, 36, 36, 36, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497101 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497101 Building ZINC001739497635 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497635 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/868 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739497635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497635 none C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 40, 50, 50, 50, 50, 50, 50, 50, 17, 6, 17, 4, 1, 4, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/869 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739497635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497635 none C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 32, 40, 50, 50, 50, 50, 50, 50, 50, 18, 6, 18, 4, 1, 4, 1, 1, 1, 2, 2, 2, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497635 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 Building ZINC001739497635 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497635 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 868) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739497635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497635 none C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 40, 50, 50, 50, 50, 50, 50, 50, 17, 6, 17, 4, 1, 4, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 869) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739497635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497635 none C[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 32, 40, 50, 50, 50, 50, 50, 50, 50, 18, 6, 18, 4, 1, 4, 1, 1, 1, 2, 2, 2, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497635 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497635 Building ZINC001739497637 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497637 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/870 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739497637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497637 none C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 41, 50, 50, 50, 50, 50, 50, 50, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/871 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739497637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497637 none C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 28, 40, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497637 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 Building ZINC001739497637 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739497637 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 870) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739497637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497637 none C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 41, 50, 50, 50, 50, 50, 50, 50, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 871) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739497637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739497637 none C[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 28, 40, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739497637 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739497637 Building ZINC001739498744 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739498744 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/872 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739498744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739498744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498744 none C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 17, 17, 47, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 39, 39, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/873 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739498744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739498744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498744 none C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 17, 17, 47, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739498744 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 Building ZINC001739498744 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739498744 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 872) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739498744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739498744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498744 none C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 17, 17, 47, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 39, 39, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 873) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739498744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739498744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498744 none C[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 17, 17, 47, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739498744 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498744 Building ZINC001739498747 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739498747 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/874 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739498747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739498747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498747 none C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 16, 16, 48, 50, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 36, 36, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/875 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739498747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739498747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498747 none C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 19, 19, 48, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739498747 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 Building ZINC001739498747 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739498747 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 874) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739498747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739498747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498747 none C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 16, 16, 48, 50, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 36, 36, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 875) grep: /scratch/xiaobo/45881/xch-8058115.60/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: C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739498747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739498747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739498747 none C[C@@H]1CN(C(=O)C[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 19, 19, 48, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739498747 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739498747 Building ZINC001739513554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739513554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/876 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739513554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513554 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 41, 17, 17, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 41, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/877 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739513554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513554 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 13, 36, 13, 13, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 36, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739513554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 Building ZINC001739513554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739513554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 876) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739513554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513554 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 41, 17, 17, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 41, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 877) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739513554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513554 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 13, 36, 13, 13, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 36, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739513554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513554 Building ZINC001739513555 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739513555 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/878 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739513555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513555 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 22, 47, 22, 22, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/879 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739513555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513555 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 42, 19, 19, 7, 7, 7, 7, 3, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 42, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739513555 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 Building ZINC001739513555 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739513555 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 878) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739513555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513555 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 22, 47, 22, 22, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 879) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O) `ZINC001739513555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739513555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739513555 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 5, 5, 1, 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, 7, 7] dock color type numbers: [7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 42, 19, 19, 7, 7, 7, 7, 3, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 42, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739513555 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739513555 Building ZINC001739565409 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565409 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/880 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739565409 none CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 25, 37, 50, 50, 50, 50, 50, 50, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/881 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739565409 none CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 10, 10, 10, 10, 10, 27, 38, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565409 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 Building ZINC001739565409 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565409 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 880) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739565409 none CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 25, 37, 50, 50, 50, 50, 50, 50, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 881) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739565409 none CO[C@@H]1CN(C(=O)C2(F)CCOCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 10, 10, 10, 10, 10, 27, 38, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565409 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565409 Building ZINC001739565521 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739565521 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/882 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/883 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/884 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/884' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/885 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/885' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565521 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 Building ZINC001739565521 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739565521 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 882) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 883) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 884) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 885) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565521 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 Building ZINC001739565521 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739565521 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 882) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 883) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 884) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 885) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565521 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 Building ZINC001739565521 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739565521 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 882) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 883) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 884) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 24, 24, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 50, 24, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 885) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565521.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739565521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001739565521 none CO[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 25, 25, 25, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 50, 25, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565521 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565521 Building ZINC001739565734 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565734 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/886 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001739565734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739565734 none CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 23, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 20, 14, 34, 34, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 14, 14, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/887 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001739565734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739565734 none CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 22, 14, 22, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 19, 14, 34, 34, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565734 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 Building ZINC001739565734 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565734 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 886) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001739565734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739565734 none CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 23, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 20, 14, 34, 34, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 14, 14, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 887) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001739565734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739565734 none CCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 22, 14, 22, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 19, 14, 34, 34, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565734 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565734 Building ZINC001739565814 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565814 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/888 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739565814 none CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 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/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/889 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739565814 none CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565814 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 Building ZINC001739565814 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565814 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 888) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739565814 none CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 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/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 889) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739565814 none CO[C@@H]1CN(C(=O)c2cnn3cc[nH]c23)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565814 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565814 Building ZINC001739565865 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565865 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/890 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739565865 none CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 18, 18, 38, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 8, 8, 38, 38, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/891 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739565865 none CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 17, 17, 40, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 9, 9, 40, 40, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565865 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 Building ZINC001739565865 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739565865 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 890) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739565865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739565865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739565865 none CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 18, 18, 38, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 8, 8, 38, 38, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 891) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739565865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739565865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739565865 none CO[C@@H]1CN(C(=O)CC2OCCCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 17, 17, 40, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 9, 9, 40, 40, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739565865 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739565865 Building ZINC001739566015 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739566015 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/892 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739566015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739566015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739566015 none CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 12, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/893 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739566015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739566015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739566015 none CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 12, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739566015 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 Building ZINC001739566015 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739566015 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 892) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739566015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739566015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739566015 none CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 12, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 893) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739566015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739566015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739566015 none CO[C@@H]1CN(C(=O)c2c(C)noc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 1, 1, 5, 8, 12, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739566015 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566015 Building ZINC001739566353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739566353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/894 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739566353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739566353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739566353 none CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 11, 11, 11, 11, 18, 18, 35, 36, 50, 50, 48, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 11, 11, 35, 35, 36, 36, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/895 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739566353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739566353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739566353 none CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 16, 16, 36, 40, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 36, 36, 40, 40, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739566353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 Building ZINC001739566353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739566353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 894) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001739566353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739566353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739566353 none CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 11, 11, 11, 11, 18, 18, 35, 36, 50, 50, 48, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 11, 11, 35, 35, 36, 36, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 895) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001739566353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739566353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739566353 none CO[C@@H]1CN(C(=O)CCc2ncccn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 16, 16, 36, 40, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 36, 36, 40, 40, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739566353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739566353 Building ZINC001739576736 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739576736 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/896 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1) `ZINC001739576736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739576736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739576736 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 32, 38, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 32, 32, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/897 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1) `ZINC001739576736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739576736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739576736 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 35, 40, 50, 50, 50, 50, 50, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 35, 35, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739576736 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 Building ZINC001739576736 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739576736 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 896) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1) `ZINC001739576736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739576736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739576736 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 32, 38, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 32, 32, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 897) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1) `ZINC001739576736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739576736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739576736 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccn(C)n1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 35, 40, 50, 50, 50, 50, 50, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 35, 35, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739576736 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739576736 Building ZINC001739577644 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739577644 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/898 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1) `ZINC001739577644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739577644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739577644 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 9, 15, 40, 50, 50, 50, 50, 50, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 15, 15, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/899 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1) `ZINC001739577644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739577644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739577644 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 13, 50, 50, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 13, 13, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739577644 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 Building ZINC001739577644 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739577644 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 898) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1) `ZINC001739577644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739577644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739577644 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 9, 15, 40, 50, 50, 50, 50, 50, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 15, 15, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 899) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1) `ZINC001739577644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739577644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001739577644 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COc1cc(C)on1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 13, 50, 50, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 13, 13, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739577644 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739577644 Building ZINC001739581801 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739581801 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/900 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1) `ZINC001739581801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739581801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739581801 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 17, 46, 50, 50, 50, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/901 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1) `ZINC001739581801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739581801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739581801 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 47, 50, 50, 50, 50, 50, 50, 14, 14, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 19, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739581801 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 Building ZINC001739581801 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739581801 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 900) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1) `ZINC001739581801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739581801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739581801 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 17, 46, 50, 50, 50, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 901) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1) `ZINC001739581801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739581801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739581801 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cncnc1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 47, 50, 50, 50, 50, 50, 50, 14, 14, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 19, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739581801 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739581801 Building ZINC001739584367 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739584367 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/902 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001739584367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739584367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739584367 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 22, 18, 18, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 40, 40, 40, 50, 50, 50, 50, 50, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/903 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001739584367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739584367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739584367 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 12, 12, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 40, 40, 40, 50, 50, 50, 50, 50, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739584367 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 Building ZINC001739584367 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739584367 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 902) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001739584367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739584367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739584367 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 22, 18, 18, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 40, 40, 40, 50, 50, 50, 50, 50, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 903) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001739584367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739584367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739584367 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 12, 12, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 40, 40, 40, 50, 50, 50, 50, 50, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739584367 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739584367 Building ZINC001739586499 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739586499 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/904 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1) `ZINC001739586499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739586499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739586499 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 32, 37, 50, 50, 50, 50, 50, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 32, 32, 37, 37, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/905 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1) `ZINC001739586499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739586499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739586499 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 20, 33, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 20, 33, 33, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739586499 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 Building ZINC001739586499 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739586499 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 904) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1) `ZINC001739586499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739586499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739586499 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 32, 37, 50, 50, 50, 50, 50, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 32, 32, 37, 37, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 905) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1) `ZINC001739586499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739586499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739586499 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1nc(C)no1 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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 20, 33, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 20, 33, 33, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739586499 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739586499 Building ZINC001739607554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/906 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739607554 none Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 29, 24, 20, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 29, 29, 29, 29, 20, 20, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/907 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739607554 none Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 27, 23, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 31, 31, 31, 31, 23, 23, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 Building ZINC001739607554 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607554 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 906) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739607554 none Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 29, 24, 20, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 29, 29, 29, 29, 20, 20, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 907) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739607554 none Cc1nccn1CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 27, 23, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 31, 31, 31, 31, 23, 23, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607554 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607554 Building ZINC001739607631 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607631 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/908 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1) `ZINC001739607631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739607631 none CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 26] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/909 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1) `ZINC001739607631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739607631 none CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 17, 9, 17, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 26] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607631 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 Building ZINC001739607631 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607631 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 908) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1) `ZINC001739607631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739607631 none CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 26] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 909) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1) `ZINC001739607631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739607631 none CCCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 17, 9, 17, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 26] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607631 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607631 Building ZINC001739607787 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607787 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/910 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739607787 none COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 35, 35, 35, 35, 35, 16, 9, 16, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/911 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739607787 none COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 33, 33, 33, 33, 33, 16, 10, 16, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607787 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 Building ZINC001739607787 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607787 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 910) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739607787 none COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 35, 35, 35, 35, 35, 16, 9, 16, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 911) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739607787 none COCc1ncsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 33, 33, 33, 33, 33, 16, 10, 16, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607787 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607787 Building ZINC001739607871 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607871 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/912 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1) `ZINC001739607871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739607871 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 12, 29, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/913 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1) `ZINC001739607871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739607871 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 13, 27, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607871 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 Building ZINC001739607871 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607871 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 912) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1) `ZINC001739607871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739607871 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 12, 29, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 913) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1) `ZINC001739607871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739607871 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 13, 27, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607871 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607871 Building ZINC001739607888 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607888 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/914 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739607888 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 27, 10, 27, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 45, 45, 45, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/915 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739607888 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 28, 10, 28, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 45, 45, 45, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607888 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 Building ZINC001739607888 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739607888 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 914) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739607888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739607888 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 27, 10, 27, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 45, 45, 45, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 915) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739607888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739607888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739607888 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 28, 10, 28, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 45, 45, 45, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739607888 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739607888 Building ZINC001739608188 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608188 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/916 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O) `ZINC001739608188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608188 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 23, 23, 32, 32, 32, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 10, 10, 30] 150 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/917 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O) `ZINC001739608188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608188 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 26, 26, 34, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 12, 12, 36] 150 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608188 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 Building ZINC001739608188 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608188 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 916) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O) `ZINC001739608188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608188 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 23, 23, 32, 32, 32, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 10, 10, 30] 150 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 917) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O) `ZINC001739608188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608188 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)c2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 26, 26, 34, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 12, 12, 36] 150 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608188 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608188 Building ZINC001739608212 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608212 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/918 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O) `ZINC001739608212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739608212 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 13, 13, 27, 29, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 29, 29, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/919 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O) `ZINC001739608212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739608212 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 14, 14, 28, 32, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 32, 32, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608212 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 Building ZINC001739608212 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608212 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 918) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O) `ZINC001739608212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739608212 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 13, 13, 27, 29, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 29, 29, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 919) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O) `ZINC001739608212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739608212 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 9, 9, 9, 9, 14, 14, 28, 32, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 32, 32, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608212 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608212 Building ZINC001739608341 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608341 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/920 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/921 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/922 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/922' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/923 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/923' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608341 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 Building ZINC001739608341 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608341 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 920) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 921) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 922) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 923) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608341 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 Building ZINC001739608341 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608341 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 920) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 921) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 922) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 923) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608341 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 Building ZINC001739608341 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608341 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 920) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 921) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 38, 27, 18, 27, 5, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 38, 38, 27, 27, 27, 18, 18, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 922) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 923) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608341.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001739608341 none CCCCCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 36, 29, 21, 29, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 36, 36, 29, 29, 29, 21, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [51, 54, 57, 55, 50, 16, 49, 18, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608341 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608341 Building ZINC001739608353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/924 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739608353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608353 none COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 28, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/925 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739608353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608353 none COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 7, 4, 7, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 28, 28, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 Building ZINC001739608353 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608353 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 924) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739608353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608353 none COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 28, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 925) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739608353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608353 none COc1cccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 7, 4, 7, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 28, 28, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608353 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608353 Building ZINC001739608369 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608369 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/926 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608369 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/927 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608369 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 11, 11, 44, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608369 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 Building ZINC001739608369 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608369 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 926) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608369 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 927) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608369 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 11, 11, 44, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608369 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608369 Building ZINC001739608370 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608370 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/928 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608370 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 13, 13, 44, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/929 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608370 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 13, 13, 45, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608370 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 Building ZINC001739608370 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608370 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 928) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608370 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 13, 13, 44, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 929) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O) `ZINC001739608370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739608370 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CC(C)(C)CO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 10, 10, 10, 10, 13, 13, 45, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608370 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608370 Building ZINC001739608374 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608374 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/930 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001739608374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608374 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 50, 44, 50, 50, 37, 13, 37, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/931 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001739608374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608374 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 46, 50, 50, 40, 15, 40, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608374 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 Building ZINC001739608374 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608374 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 930) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001739608374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608374 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 50, 44, 50, 50, 37, 13, 37, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 931) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001739608374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739608374 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 46, 50, 50, 40, 15, 40, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608374 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608374 Building ZINC001739608806 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608806 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/932 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C) `ZINC001739608806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608806 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 24, 10, 24, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/933 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C) `ZINC001739608806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608806 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 22, 10, 22, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608806 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 Building ZINC001739608806 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608806 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 932) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C) `ZINC001739608806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608806 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 24, 10, 24, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 933) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C) `ZINC001739608806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608806 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 22, 10, 22, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608806 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608806 Building ZINC001739608825 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608825 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/934 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608825 none COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 50, 50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/935 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608825 none COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 50, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608825 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 Building ZINC001739608825 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608825 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 934) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608825 none COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 50, 50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 935) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739608825 none COc1cc(C)ccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 50, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608825 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608825 Building ZINC001739608926 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608926 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/936 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/937 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/938 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/938' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/939 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/939' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608926 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 Building ZINC001739608926 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608926 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 936) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 937) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 938) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 939) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608926 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 Building ZINC001739608926 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608926 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 936) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 937) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 938) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 939) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608926 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 Building ZINC001739608926 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608926 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 936) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 937) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 938) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 939) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608926.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608926 none CCN1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608926 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608926 Building ZINC001739608932 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608932 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/940 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/941 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/942 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/942' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/943 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/943' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608932 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 Building ZINC001739608932 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608932 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 940) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 941) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 942) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 943) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608932 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 Building ZINC001739608932 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608932 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 940) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 941) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 942) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 943) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608932 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 Building ZINC001739608932 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739608932 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 940) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 941) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 942) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 943) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739608932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739608932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739608932 none CCN1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608932 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608932 Building ZINC001739608936 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608936 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/944 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O) `ZINC001739608936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739608936 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 19, 32, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 19, 19, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/945 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O) `ZINC001739608936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739608936 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 18, 32, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 18, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608936 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 Building ZINC001739608936 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739608936 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 944) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O) `ZINC001739608936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739608936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739608936 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 19, 32, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 19, 19, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 945) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O) `ZINC001739608936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739608936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001739608936 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COc2cccc(F)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 4, 4, 18, 32, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 18, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739608936 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739608936 Building ZINC001739609380 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609380 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/946 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609380 none CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 50, 16, 11, 16, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 45, 45, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/947 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609380 none CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 18, 12, 18, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 43, 43, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609380 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 Building ZINC001739609380 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609380 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 946) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609380 none CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 50, 16, 11, 16, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 45, 45, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 947) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609380 none CO[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 50, 18, 12, 18, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 43, 43, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609380 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609380 Building ZINC001739609384 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609384 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/948 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609384 none CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 50, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 44, 44, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 219 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/949 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609384 none CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609384 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 Building ZINC001739609384 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609384 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 948) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609384 none CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 50, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 44, 44, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 219 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 949) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F) `ZINC001739609384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739609384 none CO[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 42, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609384 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609384 Building ZINC001739609476 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609476 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/950 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/951 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/952 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/952' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/953 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/953' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609476 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 Building ZINC001739609476 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609476 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 950) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 951) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 952) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 953) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609476 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 Building ZINC001739609476 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609476 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 950) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 951) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 952) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 953) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609476 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 Building ZINC001739609476 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609476 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 950) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 951) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 11, 18, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 952) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 953) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609476.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609476 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609476 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609476 Building ZINC001739609479 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609479 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/954 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/955 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/956 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/956' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/957 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/957' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609479 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 Building ZINC001739609479 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609479 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 954) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 955) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 956) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 957) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609479 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 Building ZINC001739609479 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609479 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 954) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 955) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 956) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 957) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609479 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 Building ZINC001739609479 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739609479 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 954) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 955) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 956) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 957) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001739609479.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739609479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739609479 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 16, 50, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609479 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609479 Building ZINC001739609489 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609489 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/958 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1) `ZINC001739609489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609489 none COCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 16, 10, 16, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 231 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/959 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1) `ZINC001739609489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609489 none COCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 14, 8, 14, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 223 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609489 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 Building ZINC001739609489 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609489 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 958) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1) `ZINC001739609489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609489 none COCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 16, 10, 16, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 231 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 959) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1) `ZINC001739609489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609489 none COCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 14, 8, 14, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 223 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609489 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609489 Building ZINC001739609497 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609497 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/960 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001739609497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609497 none CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 34, 25, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 25, 25, 25, 50, 50, 50, 50, 50, 45, 45, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 25, 25, 25, 25, 25, 25] 150 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 231 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/961 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001739609497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609497 none CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 34, 27, 21, 9, 21, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 50, 50, 50, 50, 50, 46, 46, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 27, 27, 27, 27, 27, 27] 150 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 237 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609497 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 Building ZINC001739609497 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609497 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 960) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001739609497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609497 none CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 34, 25, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 25, 25, 25, 50, 50, 50, 50, 50, 45, 45, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 25, 25, 25, 25, 25, 25] 150 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 231 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 961) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001739609497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001739609497 none CCOCCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 34, 27, 21, 9, 21, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 50, 50, 50, 50, 50, 46, 46, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 27, 27, 27, 27, 27, 27] 150 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 237 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609497 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609497 Building ZINC001739609565 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609565 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/962 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1) `ZINC001739609565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001739609565 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', '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, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 23, 9, 23, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/963 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1) `ZINC001739609565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001739609565 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', '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, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 22, 9, 22, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609565 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 Building ZINC001739609565 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609565 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 962) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1) `ZINC001739609565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001739609565 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', '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, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 23, 9, 23, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 963) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1) `ZINC001739609565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001739609565 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', '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, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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: [50, 50, 50, 50, 22, 9, 22, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609565 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609565 Building ZINC001739609578 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609578 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/964 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O) `ZINC001739609578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739609578 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 24, 28, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/965 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O) `ZINC001739609578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739609578 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 3, 3, 3, 3, 3, 3, 9, 21, 32, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609578 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 Building ZINC001739609578 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609578 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 964) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O) `ZINC001739609578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739609578 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 24, 28, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 965) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O) `ZINC001739609578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001739609578 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCC2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 3, 3, 3, 3, 3, 3, 9, 21, 32, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609578 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609578 Building ZINC001739609959 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609959 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/966 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O) `ZINC001739609959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739609959 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 8, 8, 22, 18, 41, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 24, 24, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 229 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/967 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O) `ZINC001739609959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739609959 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 8, 8, 9, 9, 25, 22, 44, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 25, 25, 29, 29, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609959 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 Building ZINC001739609959 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609959 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 966) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O) `ZINC001739609959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739609959 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 8, 8, 22, 18, 41, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 24, 24, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 229 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 967) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O) `ZINC001739609959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001739609959 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCN2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 8, 8, 9, 9, 25, 22, 44, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 25, 25, 29, 29, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609959 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609959 Building ZINC001739609974 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609974 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/968 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001739609974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739609974 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/969 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001739609974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739609974 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 11, 27, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609974 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 Building ZINC001739609974 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739609974 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 968) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001739609974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739609974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739609974 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 969) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001739609974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739609974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739609974 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 11, 27, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739609974 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739609974 Building ZINC001739610134 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610134 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/970 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O) `ZINC001739610134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739610134 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 1, 1, 1, 8, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/971 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O) `ZINC001739610134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739610134 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 1, 1, 1, 8, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610134 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 Building ZINC001739610134 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610134 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 970) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O) `ZINC001739610134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739610134 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 1, 1, 1, 8, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 971) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O) `ZINC001739610134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001739610134 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3[nH]ccc3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 1, 1, 1, 8, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610134 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610134 Building ZINC001739610142 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610142 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/972 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739610142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739610142 none COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 25, 25, 16, 25, 25, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 25, 50, 50, 50, 50, 50, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/973 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739610142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739610142 none COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 27, 17, 27, 27, 10, 6, 10, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 26, 27, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 27] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610142 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 Building ZINC001739610142 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610142 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 972) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739610142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739610142 none COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 25, 25, 16, 25, 25, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 25, 50, 50, 50, 50, 50, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 973) grep: /scratch/xiaobo/45881/xch-8058115.60/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: COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001739610142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001739610142 none COCc1cccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 27, 17, 27, 27, 10, 6, 10, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 26, 27, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 27] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610142 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610142 Building ZINC001739610146 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610146 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/974 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001739610146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739610146 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 12, 26, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/975 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001739610146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739610146 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 12, 29, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610146 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 Building ZINC001739610146 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610146 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 974) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001739610146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739610146 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 12, 26, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 975) grep: /scratch/xiaobo/45881/xch-8058115.60/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)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001739610146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001739610146 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 12, 29, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610146 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610146 Building ZINC001739610323 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610323 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/976 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610323 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 25, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/977 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610323 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610323 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 Building ZINC001739610323 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610323 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 976) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610323 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 11, 11, 11, 11, 25, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 977) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610323 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 10, 10, 10, 10, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610323 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610323 Building ZINC001739610324 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610324 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/978 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610324 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/979 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610324 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 25, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610324 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 Building ZINC001739610324 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610324 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 978) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610324 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 12, 12, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 979) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O) `ZINC001739610324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001739610324 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2Cc3ccccc3O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 13, 13, 13, 13, 25, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610324 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610324 Building ZINC001739610330 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610330 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/980 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O) `ZINC001739610330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739610330 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 9, 9, 21, 23, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 23, 23, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/981 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O) `ZINC001739610330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739610330 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 9, 9, 27, 31, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 27, 31, 31, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610330 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 Building ZINC001739610330 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610330 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 980) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O) `ZINC001739610330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739610330 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 8, 8, 9, 9, 21, 23, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 23, 23, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 981) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O) `ZINC001739610330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001739610330 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2nccs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 7, 7, 7, 7, 9, 9, 27, 31, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 27, 31, 31, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610330 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610330 Building ZINC001739610334 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610334 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/982 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610334 none CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 30, 30, 30, 30, 30, 13, 6, 13, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/983 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610334 none CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 33, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610334 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 Building ZINC001739610334 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610334 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 982) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610334 none CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 30, 30, 30, 30, 30, 13, 6, 13, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 983) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610334 none CCCc1onc(C)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 33, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610334 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610334 Building ZINC001739610341 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610341 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/984 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001739610341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610341 none Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 11, 31, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 33, 11, 11, 50, 50, 50] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/985 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001739610341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610341 none Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610341 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 Building ZINC001739610341 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610341 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 984) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001739610341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610341 none Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 31, 11, 31, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 33, 11, 11, 50, 50, 50] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 985) grep: /scratch/xiaobo/45881/xch-8058115.60/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: Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1) `ZINC001739610341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610341 none Cc1cc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610341 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610341 Building ZINC001739610501 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610501 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/986 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610501 none CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 50, 30, 14, 30, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/987 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610501 none CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610501 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 Building ZINC001739610501 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739610501 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 986) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610501 none CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 50, 30, 14, 30, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 987) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001739610501 none CN(C)c1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610501 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610501 Building ZINC001739610617 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610617 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/988 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/989 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/990 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/990' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/991 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/991' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610617 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 Building ZINC001739610617 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610617 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 988) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 989) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 990) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 991) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610617 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 Building ZINC001739610617 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610617 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 988) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 989) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 990) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 991) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610617 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 Building ZINC001739610617 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610617 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 988) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 989) grep: /scratch/xiaobo/45881/xch-8058115.60/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 50, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 990) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 991) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610617 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610617 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610617 Building ZINC001739610621 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610621 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/992 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/993 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/994 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/994' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/995 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/995' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610621 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 Building ZINC001739610621 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610621 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 992) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 993) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 994) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 995) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610621 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 Building ZINC001739610621 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610621 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 992) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 993) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 994) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 995) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610621 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 Building ZINC001739610621 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001739610621 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 992) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 993) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 173 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `2' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 2 (index: 994) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `3' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 3 (index: 995) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001739610621.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001739610621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001739610621 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [51, 54, 49, 55, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001739610621 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 3: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/3.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/1.* 2: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/2.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001739610621 Building ZINC001556929345 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556929345 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/996 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1) `ZINC001556929345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556929345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001556929345 none O=C(CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 15, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 15, 15, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/997 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1) `ZINC001556929345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556929345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001556929345 none O=C(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 15, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 15, 15, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556929345 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 Building ZINC001556929345 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556929345 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 996) grep: /scratch/xiaobo/45881/xch-8058115.60/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: O=C(CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1) `ZINC001556929345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556929345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001556929345 none O=C(CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 15, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 15, 15, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 997) grep: /scratch/xiaobo/45881/xch-8058115.60/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: O=C(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1) `ZINC001556929345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556929345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001556929345 none O=C(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Nc1ncc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 15, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 15, 15, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001556929345 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001556929345 Building ZINC001639420296 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639420296 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/998 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/998' -> `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)CCN(C(=O)OC(C)(C)C)C2)cn1) `ZINC001639420296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639420296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639420296 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCN(C(=O)OC(C)(C)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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 10, 5, 5, 10, 10, 10, 10, 10, 5, 2, 7, 7, 30, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/999 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/999' -> `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)CCN(C(=O)OC(C)(C)C)C2)cn1) `ZINC001639420296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639420296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639420296 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCN(C(=O)OC(C)(C)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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 16, 16, 16, 16, 19, 19, 20, 20, 20, 20, 16, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 48, 16, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 16, 16, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639420296 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 Building ZINC001639420296 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639420296 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 998) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCN(C(=O)OC(C)(C)C)C2)cn1) `ZINC001639420296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639420296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639420296 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCN(C(=O)OC(C)(C)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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 10, 5, 5, 10, 10, 10, 10, 10, 5, 2, 7, 7, 30, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 mkdir: created directory `1' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/1 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 1 (index: 999) grep: /scratch/xiaobo/45881/xch-8058115.60/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCN(C(=O)OC(C)(C)C)C2)cn1) `ZINC001639420296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639420296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639420296 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCN(C(=O)OC(C)(C)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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 16, 16, 16, 16, 19, 19, 20, 20, 20, 20, 16, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 48, 16, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 16, 16, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639420296 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 1: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/1.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420296 Building ZINC001639420298 mkdir: created directory `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001639420298 mkdir: created directory `0' /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298/0 /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/45881/xch-8058115.60/working/3D/1000 `/scratch/xiaobo/45881/xch-8058115.60/working/3D/1000' -> `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)CCN(C(=O)OC(C)(C)C)C2)cn1) `ZINC001639420298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639420298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639420298 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCN(C(=O)OC(C)(C)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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 11, 15, 15, 15, 15, 15, 18, 18, 20, 20, 20, 20, 15, 6, 6, 15, 15, 15, 15, 15, 6, 3, 11, 11, 45, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298 /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Finished preparing ZINC001639420298 Recording results /scratch/xiaobo/45881/xch-8058115.60/working /scratch/xiaobo/45881/xch-8058115.60 Appending to /scratch/xiaobo/45881/xch-8058115.60/finished/xch.* 0: /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298/0.* Removing working files in /scratch/xiaobo/45881/xch-8058115.60/working/building/ZINC001639420298 /scratch/xiaobo/45881/xch-8058115.60 Compressing combined databse files /scratch/xiaobo/45881/xch-8058115.60/finished/xch.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/45881/xch-8058115.60/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/45881/xch-8058115.60/working/3D/1001' removed directory: `/scratch/xiaobo/45881/xch-8058115.60/working/3D' rmdir: removing directory, `/scratch/xiaobo/45881/xch-8058115.60/working/building' rmdir: removing directory, `/scratch/xiaobo/45881/xch-8058115.60/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/45881/xch-8058115.60' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xch' `/scratch/xiaobo/45881/xch-8058115.60/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xch/finished' `/scratch/xiaobo/45881/xch-8058115.60/finished/xch.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xch/finished/xch.db2.gz' removed `/scratch/xiaobo/45881/xch-8058115.60/finished/xch.db2.gz' removed directory: `/scratch/xiaobo/45881/xch-8058115.60/finished' removed directory: `/scratch/xiaobo/45881/xch-8058115.60'